Composition for Immunization Against Streptococcus Pneumoniae

ABSTRACT

This disclosure relates to a method of preventing or treating a recurrence of acute otitis media in a subject at risk comprising administering a therapeutically effective amount of a composition, at least once to the subject. The composition administered comprises at least one immunogenic polypeptide selected from the group consisting of  Streptococcus pneumoniae  PhtD, C PhtE, PcpA, LytB and detoxified pneumolysis

RELATED APPLICATIONS

This application is a continuation of U.S. Ser. No. 13/990,853 filed on Jun. 25, 2014, now U.S. Pat. No. 9,944,680, that was filed under 35 U.S.C. § 371 from and claims priority to International Application No. PCT/US2011/063132, filed Dec. 2, 2011, which claims priority to U.S. Ser. No. 61/510,620 filed Jul. 22, 2011 and U.S. Ser. No. 61/419,635 filed Dec. 3, 2010, the contents of each being incorporated herein by reference in their entirety.

FIELD OF THE DISCLOSURE

This disclosure relates to the field of immunology and in particular, to methods of immunization against Streptococcus pneumoniae.

BACKGROUND

Otitis media is a common disease in children. The term “otitis media” encompasses a number of clinical disorders including myringitis, otitis media with effusion (OME), chronic suppurative otitis media and acute otitis media (AOM) (24). Acute otitis media (AOM) is a symptomatic illness associated with upper respiratory symptoms, pain, fever and otorrhea. It is the most common infectious disease worldwide, leading to excessive antibiotic consumption in children in most countries and to a substantial burden of deafness and other complications in the developing countries (1-3).

AOM is fairly common and about 60-70% of children experience at least one episode of AOM during the first 3 years of their life (4,5). A subpopulation of children experience recurrent otitis media. Those who experience 3 or more episodes of AOM within 6 months or 4 infections within a year are considered otitis-prone, and represent 10-30% of the total population of children (4; 5).

Nasopharyngeal (NP) colonization with one or more otopathogens is a necessary precedent to the development of AOM. Streptococcus pneumoniae (Spn), non-typeable Haemophilus influenzae (NTHi) and Moraxella Catarrhalis are the most common otopathogens causing AOM, and of these three, Spn predominates (6). A direct relationship between frequency of colonization with NTHi and the frequency of AOM has been noted (J. Infect Dis 170:862-866).

Recurrent AOM is currently treated with different antibiotics of escalating strength on the presumption that the recurrent infections are caused by increasingly antibiotic-resistant bacteria. When recurrences occur at a frequency of 3 in 6 months or 4 in 12 months, then tymnpanostomy tube surgery is often performed, with or without concurrent adenoidectomy and/or tonsillectomy.

In regards to prophylactic measures, at present, there are two available types of pneumococcal vaccines. The first includes capsular polysaccharides from 23 types of S. pneumoniae, which together represent the capsular types of about 90% of strains causing pneumococcal infection. This vaccine, however, is not very immunogenic in young children (Fedson, and Musher 2004, “Pneumococcal Polysaccharide Vaccine”, pp. 529-588; In Vaccines. S. A. Plotikin and W. A. Orenstein (eds.), W.B. Saunders and Co., Philadelphia, Pa.; Shapiro et. al., N. Engl. J. Med. 325:1453-1460 (1991)) as they do not generate a good immune response to polysaccharide antigens prior to 2 years of age. This vaccine is not recommended for the prevention of otitis media.

Conjugate vaccines represent the second available type of pneumococcal vaccine. These vaccines which include serotype specific capsular polysaccharide antigens conjugated to a protein carrier, elicit serotype-specific protection. Currently available are 7-valent and 13-valent conjugate vaccines: the 7-valent includes 7 polysaccharide antigens (derived from the capsules of serotypes 4, 6B, 9V, 14, 18C, 19F and 23F) and the 13-valent conjugate includes 13 polysaccharide antigens (derived from the capsules of serotypes 1, 3, 5, 6A, 7F, and 19A, plus those covered by the 7-valent). 9-valent and 11-valent conjugate vaccines have also been developed and each includes serotype-specific polysaccharides in addition to those in the 7-valent (i.e., serotypes 1 and 5 in the 9-valent and types 3 and 7F in the 11-valent).

There are however limitations to conjugate vaccines. For example, as such vaccines elicit serotype-specific protection, to protect against additional serotypes of Streptococcus pneumoniae including those that dominate in the developing world, additional serotype-specific polysaccharides must be included which increases the difficulty of manufacture (Di Fabio et al., Pediatr. Infect. Dis. J. 20:959-967 (2001); Mulholland, Trop. Med. Int. Health 10:497-500 (2005)). The use of the 7-valent conjugate vaccine has also led to an increase in colonization and disease with strains of capsule types not covered by the polysaccharides included in the vaccine (Bogaert et al., Lancet Infect. Dis. 4:144-154 (2004); Eskola et al., N. Engl. J. Med. 344-403-409 (2001); Mbelle et al., J. Infect. Dis. 180:1171-1176 (1999)). As for pneumococcal otitis media, the available conjugate vaccines do not work as well in protecting against the disease as they do to against invasive disease. In addition, AOM recurrences are still possible following vaccination; for example, the subpopulation of children who are particularly prone to recurrent episodes of AOM, experience a number of recurrences and go on to become otitis prone, despite conjugate immunization.

Therefore, there is still a need for compositions for use in, and methods of, preventing or treating recurring pneumococcal AOM.

SUMMARY OF THE DISCLOSURE

Methods for preventing or treating a recurrence of AOM resulting from an S. pneumoniae infection in a subject at risk are described. A subject at risk includes for example, infants and children who have recurrent episodes of AOM (e.g., otitis prone) and those who have had AOM treatment failure. For example, methods of preventing or treating a recurrence of acute otitis media resulting from a Streptococcus pneumoniae infection in a subject at risk of developing a pneumococcal AOM reoccurrence, the method comprising administering at least once to said subject, a therapeutically effective amount of a composition comprising at least one isolated and purified immunogenic polypeptide selected from the group consisting of Streptococcus pneumoniae PhtD, PhtE, PcpA, LytB and detoxified pneumolysin, or an immunogenic fragment thereof, are provided. In certain embodiments, the subject may have previously experienced at least one episode of acute otitis media. In some embodiments, the subject may have experienced 3 or more episodes of acute otitis media within a period of six months or has experienced 4 or more episodes of acute otitis media within a period of 12 months. In some embodiments, the subject may have acute otitis media.

Compositions for use in these methods, in preventing or treating a recurrence of AOM are also described. The compositions comprise at least one immunogenic polypeptide of S. pneumoniae selected from the group consisting of PhtD, PhtE, PcpA, LytB, and detoxified pneumolysin, or immunogenic fragments thereof.

The subject matter disclosed herein provides several advantages. For example, the methods described herein can be used to elicit or enhance the production of antigen specific CD4+ T-cells.

Other features and advantages will be apparent from the following Detailed Description, the Drawings and the Claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The disclosure may be further understood from the following description with reference to the drawings.

FIGS. 1A-D. Graphical representation showing percent frequencies of CD45RALow memory CD4+ T-cell subsets producing various cytokines against six pneumococcal antigens: FIG. 1A: IFN-γ; FIG. 1B: IL-4; FIG. 1C: IL-2; FIG. 1D: IL-17a; in the circulation of non otitis-prone and otitis-prone children against various pneumococcal antigens. Bar graphs represent mean percentage values of CD69+CD4+ T-cells, following antigen stimulations. Error bars represent SEM, P values were calculated using Mann Whitney test. *P<0.05; **P<0.005.

FIGS. 2A-E. Graphical representation showing the comparison of IgG responses to five pneumococcal protein antigens (FIG. 2A: PhtD; FIG. 2B: LytB; FIG. 2C: PcpA; FIG. 2D: PhtE; and, FIG. 2E: Ply) in the serum samples of two cohorts of non-otitis-prone and otitis-prone children. *P<0.05; **P<0.005; ***P<0.0005. Y-axis represents Geometric mean titers and error bars are upper 95% confidence intervals.

FIGS. 3A-D. Graphical representation showing CD4+ T-cell response to SEB. PBMC samples from non-otitis-prone and otitis-prone children were stimulated with SEB and cytokine production was observed in CD45RALow CD4+ T-cell population. FIG. 3A: IFN-γ; FIG. 3B: IL-4; FIG. 3C: IL-2; FIG. 3D: IL-17a.

FIGS. 4A-E. Graphical representation showing the comparison of IgG antibody in the serum samples of children at their acute visit of AOM in 35 otitis prone, 25 AOMTF and 34 non-otitis prone children. Note: All the antibody concentrations against five proteins are in end point titers. Lines are shown to indicate significant difference observed between the two groups. *** means p value<0.0001, ** means p value<0.001, and * means p value<0.05. FIG. 4A: PhtD; FIG. 4B: LytB; FIG. 4C: PcpA; FIG. 4D: PhtE; FIG. 4E: Ply.

FIGS. 5A-J. Graphical representation showing the comparison of IgG antibody level with age (6-24 months) against five proteins of S. pneumoniae in non-otitis prone and otitis prone children. The numbers of sera included at 6, 9, 12, 15, 18 and 24 months time points were 107, 88, 65, 61, 55, and 44 respectively for the non-otitis prone children 10, 10, 9, 10, 10 and 4 respectively for the otitis prone children. Significant difference for all the five proteins except LytB (p<0.07), comparing relative rise in IgG serum antibody over time was found in non-otitis prone children while the difference was not significant in otitis prone children (p=0.40 for protein PhtD, p=0.39 for LytB, p=0.11 for PcpA, p=0.09 for PhtE and p=0.42 for Ply). FIG. 5A: IgG to PhtD; FIG. 5B: IgG to LytB; FIG. 5C: IgG to PcpA; FIG. 5D: IgG to PhtE; FIG. 5E: IgG to PlyD1; FIG. 5F: IgG to PhtD; FIG. 5G: IgG to LytB; FIG. 5H: IgG to PcpA; FIG. SI: IgG; FIG. 5J: IgG to PlyD1.

FIGS. 6A-C. FIG. 6A shows percent frequencies of antigen-specific memory B cells; FIG. 6B shows a comparison of IgG responses to five pneumococcal antigens in the serum samples of non-otitis-prone and otitis-prone children (Y-axis represents Geometric mean titers and error bars are upper 95% confidence intervals); FIG. 6C shows the correlation between the percentage of circulating PhtD-specific memory B-cells (x-axis) with serum PhtD-specific IgG concentration (y-axis).

DETAILED DESCRIPTION

Methods for preventing and/or treating a recurrence of acute otitis media resulting from an S. pneumoniae infection in a subject at risk (e.g., a child) are described. Compositions for use in these methods, in preventing and/or treating a recurrence of acute otitis media are also described. The compositions comprise at least one immunogenic polypeptide of S. pneumoniae selected from the group consisting of PhtD, PhtE, PcpA, LytB, and detoxified pneumolysin, or immunogenic fragments thereof. These methods and compositions are described further, below.

The prophylactic and therapeutic methods provided comprise the administration of a therapeutically effective amount of a composition (e.g., a pharmaceutical composition), at least once, comprising at least one isolated and purified immunogenic polypeptide of S. pneumoniae selected from the group consisting of PhtD, PhtE, PcpA, LytB, and detoxified pneumolysin, or an immunogenic fragment thereof, to subjects at risk of developing a pneumococcal AOM recurrence (i.e., a symptomatic S. pneumoniae infection resulting in an AOM recurrence).

The population of subjects at risk include, for example, infants and children that have had at least one, two, three, four or more AOM episodes in their lifetime; infants and children who are otitis prone (i.e., who have had 3 or more episodes of AOM within 6 months or 4 or more episodes of AOM within a year); and infants and children that have or who have had AOM treatment failure (i.e., those with AOM that have failed to achieve bacterial eradication and/or resolution of symptoms after at least 48 hours of appropriate antibiotic therapy; or infants and children whose signs and symptoms of AOM returned within 14 days of completing an antibiotic treatment course). The population of subjects at risk also includes for example, infants and children: with a genetic propensity for recurrent AOM (Casselbrant M L et al JAMA 1999; 282:2125-2130); attending day care outside the home; attending family day care; with one or more parents/caregivers who smoke; using a pacifier; formula rather than breast fed; and who have experienced an AOM infection in the first 6 months of life (Bentdal et al Int. J. Ped. Otorhinolaryngol. 2007; 71:1251-1259). As children age, they become less prone to AOM because of anatomical changes in the eustachion tube. Usually, the otitis prone child “outgrows” their propensity around age 3 to 5 years (40; 48-51). In certain embodiments, the subject has, or is at risk of developing, pneumococcal AOM.

As discussed in the Examples herein, otitis prone children (i.e., a population of subjects at risk) as compared to non-otitis prone children display immunological hyporesponsiveness against Spn antigens (e.g., PhtD, PhtE, PcpA, LytB, Ply). For example, as compared to non-otitis prone children, otitis prone children have a lack or reduction of pneumococcal antigen specific functional memory CD4+ T-cells (e.g., functional memory CD4+ T-cells specific for PhtD, PhtE, PcpA, LytB, or Ply) and reduced serum IgG levels to pneumococcal antigens (e.g., to PhtD, PhtE, PcpA, LytB, Ply). These children are not however deficient in total functional memory T-cells or in eliciting B cell mediated antibody responses against vaccinated antigens. Children with AOM treatment failure (AOMTF) behave immunologically similar to otitis prone children. Subjects at risk are those who display such immunological hyporesponsiveness against Spn antigens such as for example, PhtD, PhtE, PcpA, LytB and/or Ply.

As used herein, preventing a recurrence of AOM in a subject is intended to mean administration of a therapeutically effective amount of a composition decsribd herein to a subject in order to protect the subject from the development of a recurrence of pneumococcal acute otitis media.

As used herein, treating a recurrence of AOM (or an otitis prone subject or a subject with recurring AOM) is intended to mean administration of a therapeutically effective amount of a composition described herein to a subject that is afflicted with AOM caused by S. pneumoniae or that has been exposed to S. pneumoniae, and was previously afflicted with AOM, where the purpose is to cure, heal, alleviate, relieve, alter, remedy, ameliorate, improve, or affect the condition (e.g., AOM) or the symptoms of the disease (i.e., AOM).

A therapeutically effective amount refers to an amount that provides a therapeutic effect for a given condition and administration regimen. A therapeutically effective amount can be determined by the ordinary skilled medical worker based on patient characteristics (age, weight, gender, condition, complications other diseases etc.). The therapeutically effective amount will be further influenced by the route of administration of the composition.

In certain examples, the administration of the composition elicits or enhances the production of antigen specific CD4+ T-cells. The antigen specific CD4+ T-cells whose production is elicited or enhanced may be those that produce the cytokines IFN-γ, IL-4, IL-2 and/or IL-17a, for example. For example, in one embodiment, administration of the composition elicits or enhances the production of antigen specific CD4+ T-cells that produce IFN-γ. As used herein, “elicits or enhances the production of antigen specific CD4+ T-cells” is intended to mean that the quantity or percentage (%) of the antigen specific CD4+ T-cells is increased. The quantity of cells may increase by, for example, 25%, 30%, 35%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200%, 300%, 400% or more over the quantity of cells existing immediately before the administration of the composition.

In one embodiment, the administration of the composition elicits or enhances antigen specific antibody (e.g., IgG) production. By eliciting or enhancing antibody production, the total concentration (titer) of antigen specific total IgG is increased relative to the concentration (titer) existing immediately before administration. The end point dilution titer may increase by, for example, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 150%, 200% or more over the titer existing immediately before the administration of the composition. In one embodiment, the antigen specific IgG titer is increased, for example, 2, 3, or 4 fold relative to the titer existing immediately before the administration of the composition.

Also disclosed, is a method of reducing the risk of an acute otitis media recurrence in a subject at risk (e.g., a child) comprising administering to the subject a composition comprising one or more of the disclosed immunogenic polypeptides. The risk of such a recurrence may be reduced by the methods described herein.

In particular embodiments, a method of preventing or treating the otitis prone condition in a subject at risk (i.e., a subject who has had at least one or more recurring episodes of AOM) is provided.

The present disclosure also provides methods of eliciting an immune response in a subject at risk by administering the compositions described herein. This may be achieved by the administration of a pharmaceutically acceptable formulation of the composition to the subject to effect exposure of the at least one immunogenic polypeptide to the immune system of the subject.

This disclosure also provides for the use of one or more immunogenic S. pneumoniae polypeptides in compositions such as, for example, vaccine compositions. Such a composition upon administration to a subject (e.g., a mammal), induces or enhances an immune response directed against the immunogenic polypeptide (i.e., antigen) included in the composition. This response may include the generation of antibodies (e.g., through the stimulation of B cells) or a T cell-based response (e.g., a cytolytic response). These responses may or may not be protective or neutralizing. A protective or neutralizing immune response is one that is detrimental to the infectious organism corresponding to the antigen (e.g., from which the antigen was derived) and beneficial to the subject (e.g., by reducing or preventing infection). As used herein, protective or neutralizing antibodies may be reactive to the corresponding wild-type S. pneumoniae polypeptide and may reduce or inhibit the lethality of the corresponding S. pneumoniae organism or of the corresponding wild-type S. pneumoniae polypeptide when tested in subjects (e.g., mammals). An immunological composition that, upon administration to a subject, results in a protective or neutralizing immune response may be considered a vaccine. The compositions described herein find use in methods of preventing or treating an AOM recurrence in a subject at risk, whom as defined above is at risk of being infected with S. pneumoniae and developing an AOM recurrence. The composition also finds use in methods of preventing or treating recurring AOM.

The compositions described herein can be administered by an appropriate route such as for example, percutaneous (e.g., intramuscular, intravenous, intraperitoneal or subcutaneous), transdermal, mucosal (e.g., intranasal) or topical, in amounts and in regimes determined to be appropriate by one skilled in the art. For example, 100 ng-500 μg, 1-240 μg, 10-100 μg, 5-50 μg, or 10-25 μg of the immunogenic polypeptide can be administered per dose. For the purposes of prophylaxis or therapy, the vaccine can be administered once or multiple times. For example, the vaccine can be administered 1, 2, 3, or 4 times, for example. In one example, the one or more administrations may occur as part of a so-called “prime-boost” protocol. When multiple doses are administered, the doses can be separated from one another by, for example, one week, one month or several months.

The immunogenic polypeptides described herein have immunogenic activity. The term “immunogenic activity” refers to the ability of a polypeptide to elicit an immunological response in a subject (e.g., a mammal). An immunological response to a polypeptide is the development in an animal of a cellular and/or antibody-mediated immune response to the polypeptide. Usually, an immunological response includes but is not limited to one or more of the following effects: the production of antibodies, B cells, helper T cells, suppressor T cells and/or cytotoxic T cells, directed to an epitope or epitopes of the polypeptide. The term “epitope” refers to the site on an antigen to which specific B cells and/or T cells respond so that antibody is produced. The immunogenic activity may be protective. The term “protective immunogenic activity” refers to the ability of a polypeptide to elicit an immunological response in a subject that prevents or inhibits infection by S. pneumoniae (e.g., inhibits an infection by S. pneumoniae resulting in a recurrence of AOM).

In certain embodiments, a multi-component composition comprising two, three, four or more immunogenic polypeptides may be formulated to protect against a recurrence of AOM resulting from an S. pneumoniae infection. A preferred embodiment of such a composition comprises immunogenic polypeptides of PhtD and PcpA. A further preferred composition comprises immunogenic polypeptides of PhtD, PcpA and detoxified pneumolysin. Certain preferred multi-component compositions for use as described herein are described in WO2011/075823 (filed on 20 Dec. 2010 and entitled, Immunogenic Compositions).

The components of a multi-component composition preferably are compatible and are combined in appropriate ratios to avoid antigenic interference and to optimize any possible synergies. For example the amounts of each component can be in the range of about 5 μg to about 500 μg per dose, 5 μg to about 10 μg per dose, 25 μg to about 50 μg per dose or 50 μg to about 100 μg per dose. Most preferably, the range can be about 10 μg to 50 μg per antigenic component per dose.

Immunogenic Polypeptides

The nucleic acids encoding the immunogenic polypeptides may be isolated for example, but without limitation from wild type or mutant S. pneumoniae cells or alternatively, may be obtained directly from the DNA of an S. pneumoniae strain carrying the applicable DNA gene sequence (e.g., pcpA or phtD), by using the polymerase chain reaction (PCR) or by using alternative standard techniques that are recognized by one skilled in the art. Possible strains of use include for example S. pneumoniae strains TIGR4 and 14453. In preferred embodiments the polypeptides are recombinantly derived from S. pneumoniae strain 14453.

The polypeptides described herein can be produced using standard molecular biology techniques and expression systems (see for example, Molecular Cloning: A Laboratory Manual, Third Edition by Sambrook et. al., Cold Spring Harbor Press, 2001). For example, a fragment of a gene that encodes an immunogenic polypeptide may be isolated and the polynucleotide encoding the immunogenic polypeptide may be cloned into any commercially available expression vector (such as, e.g., pBR322, and pUC vectors (New England Biolabs, Inc., Ipswich, Mass.)) or expression/purification vectors (such as e.g., GST fusion vectors (Pfizer, Inc., Piscataway, N.J.)) and then expressed in a suitable prokaryotic, viral or eukaryotic host. Purification may then be achieved by conventional means, or in the case of a commercial expression/purification system, in accordance with manufacturer's instructions.

Alternatively, the immunogenic polypeptides described herein, including variants, may be obtained through chemical synthesis using commercially automated procedures, such as for example, exclusive solid phase synthesis, partial solid phase methods, fragment condensation or solution synthesis.

Immunogenic PcpA polypeptides comprise the full-length PcpA amino acid sequence (in the presence or absence of the signal sequence), fragments thereof, and variants thereof. PcpA polypeptides suitable for use in the compositions described herein include, for example, those of GenBank Accession Nos. CAB04758, YP817353, AAK76194, NP359536, ZP01835022, and ZP01833419, and those described herein and in the Examples below, among others. In one embodiment, PcpA has the amino acid sequence shown in SEQ ID NOs:1 or 2.

The amino acid sequence of full length PcpA in the S. pneumoniae 14453 genome is SEQ ID NO. 1. Preferred PcpA polypeptides may comprise an amino acid sequence having 50% or more identity (e.g, 60, 65, 70, 75, 80, 85, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99.5% or more) to SEQ ID NOs: 1, 2 or 3. Preferred polypeptides may comprise a fragment of at least 8, 9, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more, for example, consecutive amino acids of SEQ ID NOs:1, 2 or 3. Preferred fragments comprise an epitope from SEQ ID NOs.1, 2 or 3. Other preferred fragments lack one or more amino acids from the N-terminus of SEQ ID NOs: 1 or 2 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) and/or one or more amino acids from the C-terminus of SEQ ID NOs:1 or 2 while retaining at least one epitope of SEQ ID NOs:1 or 2. Further preferred fragments lack the signal sequence from the N-terminus of SEQ ID NOs: 1 or 2. A preferred PcpA polypeptide is SEQ ID NO: 3.

(PcpA, Spn strain 14453) SEQ ID NO: 1 MKKTTILSLTTAAVILAAYVPNEPILADTPSSEVIKETKVGSIIQQNNIK YKVLTVEGNIRTVQVGNGVTPVEFEAGQDGKPFTIPTKITVGDKVFTVTE VASQAFSYYPDETGRIVYYPSSITIPSSIKKIQKKGFHGSKAKTIIFDKG SQLEKIEDRAFDFSELEEIELPASLEYIGTSAFSFSQKLKKLTFSSSSKL ELISHEAFANLSNLEKLTLPKSVKTLGSNLFRLTTSLKHVDVEEGNESFA SVDGVLFSKDKTQLIYYPSQKNDESYKTPKETKELASYSFNKNSYLKKLE LNEGLEKIGTFAFADAIKLEEISLPNSLETIERLAFYGNLELKELILPDN VKNFGKHVMNGLPKLKSLTIGNNINSLPSFFLSGVLDSLKEIHIKNKSTE FSVKKDTFAIPETVKFYVTSEHIKDVLKSNLSTSNDIIVEKVDNIKQETD VAKPKKNSNQGVVGWVKDKGLWYYLNESGSMATGWVKDKGLWYYLNESGS MATGWVKDKGLWYYLNESGSMATGWVKDKGLWYYLNESGSMATGWVKDKG LWYYLNESGSMATGWVKDKGLWYYLNESGSMATGWVKDKGLWYYLNESGS MATGWFTVSGKWYYTYNSGDLLVNITTPDGYRVNANGEWVG (PcpA) SEQ ID NO: 2 MKKTTILSLTTAAVILAAYVPNEPILAAYVPNEPILADTPSSEVIKETKV GSIIQQNNIKYKVLTVEGNIGTVQVGNGVTPVEFEAGQDGKPFTIPTKIT VGDKVFTVTEVASQAFSYYPDETGRIVYYPSSITIPSSIKKIQKKGFHGS KAKTIIFDKGSQLEKIEDRAFDFSELEEIELPASLEYIGTSAFSFSQKLK KLTFSSSSKLELISHEAFANLSNLEKLTLPKSVKTLGSNLFRLITSLNML MLRGMIVASVDGVSFQSKTQLIYYPSQKNDESYKTPKETKELASYSFNKN SYLKKLELNEGLQKIGTFAFADATKLEEISLPNSLETIERLAFYGNLELK ELILPDNVKNFGKHVMNGLPKFLTLSGNNINSLPSFFLSGVLDSLKEIHI KNKSTEFSVKKDTFAIPETVKFYVTSEHIKDVLKSNLSTSNDIIVEKVDN IKQETDVAKPKKNSNQGVVGWVKDKGLWYYLNESGSMATGWVKDKGLWYY LNESGSMATGWVKDKGLWYYLNESGSMATGWVKDKGLWYYLNESGSMATG WVKDKGLWYYLNESGSMATGWVKDKGLWYYLNESGSMATGWVKDKGLWYY LNESGSMATGWVKDKGLWYYLNESGSMATGWVKDKGLWYYLNESGSMATG WVKDKGLWYYLNESGSMATGWVKDKGLWYYLNESGSMATGWFKVSGKWYY TYNSGDFI (PcpA construct) SEQ ID NO: 3 MADTPSSEVIKETKVGSIIQQNNIKYKVLTVEGNIGTVQVGNGVTPVEFE AGQDGKPFTIPTKITVGDKVFTVTEVASQAFSYYPDETGRIVYYPSSITI PSSIKKIQKKGFHGSKAKTIIFDKGSQLEKIEDRAFDFSELEEIELPASL EYIGTSAFSFSQKLKKLTFSSSSKLELISHEAFANLSNLEKLTLPKSVKI LGSNLFRLITSLKHVDVEEGNESFASVDGVLFSKDKTQLIYYPSQKNDES YKTPKETKELASYSFNKNSYLKKLELNEGLEKIGTFAFADAIKLEEISLP NSLETIERLAFYGNLELKELILPDNVKNFGKHVMNGLPKLKSLTIGNNIN SLPSFFLSGVLDSLKEIHIKNKSTEFSVKKDTFAIPETVKFYVTSEHIKD VLKSNLSTSNDIIVEKVDNIKQETDVAKPKKNSNQGVVGWVKDKG

An immunogenic polypeptide of PcpA optionally lacks the choline binding domain anchor sequence typically present in the naturally occurring mature PcpA protein. The naturally occurring sequence of the choline binding anchor of the mature PcpA protein is disclosed in WO 2008/022302 as SEQ ID NO:52. More particularly, an immunogenic polypeptide comprises an N-terminal region of naturally occurring PcpA with one or more amino acid substitutions and about 60 to about 99% sequence identity or any identity in between, e.g. 80, 85, 90 and 95% identity, to the naturally occurring PcpA. The N-terminal region may comprise the amino acid sequence of SEQ ID NOs: 1 or 2 (or SEQ ID NOs: 1, 2, 3, 4, 41 or 45 of WO2008/022302), in the presence or absence of one or more conservative amino acid substitutions and in the presence or absence of the signal sequence. The N-terminal region may comprise an amino acid sequence having about 60 to about 99% sequence identity (or any identity in between 80 to 99% identity) to SEQ ID NOs: 1, 2 or 3 (set out in the Sequence Listing herein) or SEQ ID NOs:1, 2, 3, 4, or 41 of WO2008/022302.

Immunogenic fragments of SEQ ID NOs: 1, 2 or 3 may comprise, for example, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190 and 191 amino acid residues of SEQ ID NOs: 1, 2 or 3 or any number of amino acid residues between 5 and 191. Examples of immunogenic fragments of PcpA are disclosed in WO 2008/022302.

Variants of the immunogenic polypeptides described herein may comprise one or more conservative amino acid substitutions. Variants of the immunogenic PcpA polypeptides include amino acid sequence having about 50 to about 99% sequence identity (or any identity in between 50 and 99% identity) to SEQ ID NOs:1, 2 or 3 or any fragment thereof. Variants are selected for their immunogenic capacity using methods well known in the art.

Immunogenic PhtX polypeptides suitable for the compositions described herein include for example, the full-length PhtD or PhtE amino acid sequence (in the presence or absence of the signal sequence), immunogenic fragments thereof, variants thereof and fusion proteins thereof. PhtD polypeptides suitable for use in the compositions described herein include, for example, those of GenBank Accession Nos. AAK06760, YP816370 and NP35851, among others. The amino acid sequence of full length PhtD in the S. pneumoniae 14453 genome is SEQ ID NO: 4 and that from the TIGR4 strain is SEQ ID NO: 5. A preferred polypeptide of PhtD (derived from the S. pneumoniae 14453 genome) is SEQ ID NO: 6. PhtE polypeptides suitable for use in the composition described herein include, for example, those of GenBank Accession Nos. AAK06761, YP816371 and NP358502, among others. The amino acid sequence of full length PhtE in the S. pneumoniae 14453 genome is SEQ ID NO: 7. A preferred polypeptide of PhtE (derived from the S. pneumoniae 14453 genome) is SEQ ID NO: 8.

(PhtD Spn strain 14453) SEQ ID NO: 4 MKINKKYLAGSVAVLALSVCSYELGRHQAGQVKKESNRVSYIDGDQAGQK AENLTPDEVSKREGINAEQIVIKITDQGYVTSHGDHYHYYNGKVPYDAII SEELLMKDPNYQLKDSDIVNEIKGGYVIKVDGKYYVYLKDAAHADNIRTK EEIKRQKQEHSHNHNSRADNAVAAARAQGRYTTDDGYIFNASDIIEDTGD AYIVPHGDHYHYIPKNELSASELAAAEAYWNGKQGSRPSSSSSYNANPVQ PRLSENHNLTVTPTYHQNQGENISSLLRELYAKPLSERHVESDGLIFDPA QITSRTARGVAVPHGNHYHFIPYEQMSELEKRIARIIPLRYRSNHWVPDS RPEQPSPQSTPEPSPSLQPAPNPQPAPNSPIDEKLVKEAVRKVGDGYVFE ENGVSRYIPAKDLSAETAAGIDSKLAKQESLSHKLGAKKTDLPSSDREFY NKAYDLLARIHQDLLDNKGRQVDFEVLDNLLERLKDVSSDKVKLVDDILA FLAPIRHPERLGKPNAQITYTDDEIQVAKLAGKYTTEDGYIFDPRDITSD EGDAYVTPHMTHSHWIKKDSLSEAERAAAQAYAKEKGLTPPSTDHQDSGN TEAKGAEAIYNRVKAAKKVPLDRMPYNLQYTVEVKNGSLIIPHYDHYHNI KFEWFDEGLYEAPKGYSLEDLLATVKYYVEHPNERPHSDNGFGNASDHVR KNKADQDSKPDEDKEHDEVSEPTHPESDEKENHAGLNPSADNLYKPSTDT EETEEEAEDTTDEAEIPQVENSVINAKIADAEALLEKVTDPSIRQNAMET LTGLKSSLLLGTKDNNTISAEVDSLLALLKESQPAPIQ (PhtD Spn strain TIGR4) SEQ ID NO: 5 MKINKKYLAGSVAVLALSVCSYELGRHQAGQVKKESNRVSYIDGDQAGQK AENLTPDEVSKREGINAEQIVIKITDQGYVTSHGDHYHYYNGKVPYDAII SEELLMKDPNYQLKDSDIVNEIKGGYVIKVDGKYYVYLKDAAHADNIRTK EEIKRQKQEHSHNHGGGSNDQAVVAARAQGRYTTDDGYIFNASDIIEDTG DAYIVPHGDHYHYIPKNELSASELAAAEAYWNGKQGSRPSSSSSYNANPA QPRLSENHNLTVITTYHQNQGENISSLLRELYAKPLSERHVESDGLIFDP AQITSRTARGVAVPHGNHYHFIPYEQMSELEKRIARIIPLRYRSNHWVPD SRPEQPSPQSTPEPSPSPQPAPNPQPAPSNPIDEKLVKEAVRKVGDGYVF EENGVSRYIPAKDLSAETAAGIDSKLAKQESLSHKLGAKKTDLPSSDREF YNKAYDLLARIHQDLLDNKGRQVDFEALDNLLERLKDVPSDKVKLVDDIL AFLAPIRHPERLGKPNAQITYTDDEIQVAKLAGKYTTEDGYIFDPRDITS DEGDAYVTPHMTHSHWIKKDSLSEAERAAAQAYAKEKGLTPPSTDHQDSG NTEAKGAEAIYNRVKAAKKVPLDRMPYNLQYTVEVKNGSLIIPHYDHYHN IKFEWFDEGLYEAPKGYTLEDLLATVKYYVEHPNERPHSDNGFGNASDHV RKNKVDQDSKPDEDKEHDEVSEPTHPESDEKENHAGLNPSADNLYKPSTD TEETEEEAEDTTDEAEIPQVENSVINAKIADAEALLEKVTDPSIRQNAME TLTGLKSSLLLGTKDNNTISAEVDSLLALLKESQPAPIQ (PhtD construct derived from Spn strain 14453) SEQ ID NO: 6 MGSYELGRHQAGQVKKESNRVSYIDGDQAGQKAENLTPDEVSKREGINAE QIVIKITDQGYVTSHGDHYHYYNGKVPYDAIISEELLMKDPNYQLKDSDI VNEIKGGYVIKVDGKYYVYLKDAAHADNIRTKEEIKRQKQEHSHNHNSRA DNAVAAARAQGRYTTDDGYIFNASDIIEDTGDAYIVPHGDHYHYIPKNEL SASELAAAEAYWNGKQGSRPSSSSSYNANPVQPRLSENHNLTVITTYHQN QGENISSLLRELYAKPLSERHVESDGLIFDPAQITSRTARGVAVPHGNHY HFIPYEQMSELEKRIARIIPLRYRSNHWVPDSRPEQPSPQSTPEPSPSLQ PAPNPQPAPSNPIDEKLVKEAVRKVGDGYVFEENGVSRYIPAKDLSAETA AGIDSKLAKQESLSHKLGAKKTDLPSSDREFYNKAYDLLARIHQDLLDNK GRQVDFEVLDNLLERLKDVSSDKVKLVDDILAFLAPIRHPERLGKPNAQI TYTDDEIQVAKLAGKYTTEDGYIFDPRDITSDEGDAYVTPHMTHSHWIKK DSLSEAERAAAQAYAKEKGLTPPSTDHQDSGNTEAKGAEAIYNRVKAAKK VPLDRMPYNLQYTVEVKNGSLIIPHYDHYHNIKFEWFDEGLYEAPKGYSL EDLLATVKYYVEHPNERPHSDNGFGNASDHVRKNKADQDSKPDEDKEHDE VSEPTHPESDEKENHAGLNPSADNLYKPSTDTEETEEEAEDTTDEAEIPQ VENSVINAKIADAEALLEKVTDPSIRQNAMETLTGLKSSLLLGTKDNNTI SAEVDSLLALLKESQPAPIQ (PhtE) SEQ ID NO: 7 MKFSKKYIAAGSAVIVSLSLCAYALNQHRSQENKDNNRVSYVDGSQSSQK SENLTPDQVSQKEGIQAEQIVIKITDQGYVTSHGDHYHYYNGKVPYDALF SEELLMKDPNYQLKDADIVNEVKGGYIIKVDGKYYVYLKDAAHADNVRTK DEINRQKQEHVKDNEKVNSNVAVARSQGRYTTNDGYVFNPADIIEDTGNA YIVPHGGHYHYIPKSDLSASELAAAKAHLAGKNMQPSQLSYSSTASDNNT QSVAKGSTSKPANKSENLQSLLKELYDSPSAQRYSESDGLVFDPAKIISR TPNGVAIPHGDHYHFIPYSKLSALEEKIARMVPISGTGSTVSTNAKPNEV VSSLGSLSSNPSSLITSKELSSASDGYIFNPKDIVEETATAYIVRHGDHF HYIPKSNQIGQPTLPNNSLATPSPSLPINPGTSHEKHEEDGYGFDANRII AEDESGFVMSHGDHNHYFFKKDLTEEQIKAAQKHLEEVKTSHNGLDSLSS HEQDYPSNAKEMKDLDKKIEEKIAGIMKQYGVKRESIVVNKEKNAIIYPH GDHHHADPIDEHKPVGIGHSHSNYELFKPEEGVAKKEGNKVYTGEELTNV VNLLKNSTFNNQNFTLANGQKRVSFSFPPELEKKLGINMLVKLITPDGKV LEKVSGKVFGEGVGNIANFELDQPYLPGQTFKYTIASKDYPEVSYDGTFT VPTSLAYKMASQTIFYPFHAGDTYLRVNPQFAVPKGTDALVRVFDEFHGN AYLENNYKVGEIKLPIPKLNQGTTRTAGNKIPVTFMANAYLDNQSTYIVE VPILEKENQTDKPSILPQFKRNKAQENLKLDEKVEEPKTSEKVEKEKLSE TGNSTSNSTLEEVPTVDPVQEKVAKFAESYGMKLENVLFNMDGTIELYLP SGEVIKKNMADFTGEAPQGNGENKPSENGKVSTGTVENQPTENKPADSLP EAPNEKPVKPENSTDNGMLNPEGNVGSDPMLDPALEEAPAVDPVQEKLEK FTASYGLGLDSVIFNMDGTIELRLPSGEVIKKNLSDLIA (PhtE construct derived from Spn strain 14453) SEQ ID NO: 8 MGKNMQPSQLSYSSTASDNNTQSVAKGSTSKPANKSENLQSLLKELYDSP SAQRYSESDGLVFDPAKIISRTPNGVAIPHGDHYHFIPYSKLSALEEKIA RMVPISGTGSTVSTNAKPNEVVSSLGSLSSNPSSLITSKELSSASDGYIF NPKDIVEETATAYIVRHGDHFHYIPKSNQIGQPTLPNNSLATPSPSLPIN PGTSHEKHEEDGYGFDANRIIAEDESGFVMSHGDHNHYFFKKDLTEEQIK AAQKHLEEVKTSHNGLDSLSSHEQDYPGNAKEMKDLDKKIEEKIAGIMKQ YGVKRESIVVNKEKNAIIYPHGDHHHADPIDEHKPVGIGHSHSNYELFKP EEGVAKKEGNKVYTGEELTNVVNLLKNSTFNNQNFTLANGQKRVSFSFPP ELEKKLGINMLVKLITPDGKVLEKVSGKVFGEGVGNIANFELDQPYLPGQ TFKYTIASKDYPEVSYDGTFTVPTSLAYKMASQTIFYPFHAGDTYLRVNP QFAVPKGTDALVRVFDEFHGNAYLENNYKVGEIKLPIPKLNQGTTRTAGN KIPVTFMANAYLDNQSTYIVEVPILEKENQTDKPSILPQFKRNKAQENSK LDEKVEEPKTSEKVEKEKLSETGNSTSNSTLEEVPTVDPVQEKVAKFAES YGMKLENVLFNMDGTIELYLPSGEVIKKNMADFTGEAPQGNGENKPSENG KVSTGTVENQPTENKPADSLPEAPNEKPVKPENSTDNGMLNPEGNVGSDP MLDPALEEAPAVDPVQEKLEKFTASYGLGLDSVIFNMDGTIELRLPSGEV IKKNLSDFIA

Immunogenic PhtX (e.g., PhtD or PhtE) polypeptides may include the full length protein with the signal sequence attached, the mature full length protein with the signal peptide (e.g., about 20 amino acids at N-terminus) removed, variants of PhtX (naturally occurring or otherwise, e.g., synthetically derived) and immunogenic fragments of PhtX (e.g, fragments comprising at least 15 or 20 contiguous amino acids present in the naturally occurring mature PhtX protein). The immunogenic fragments and variants of PhtX polypeptides are capable of eliciting an immune response specific for the corresponding full length mature amino acid sequence. Examples of immunogenic fragments of PhtD are disclosed in PCT publication WO2009/012588.

Preferred PhtD polypeptides for use may comprise an amino acid sequence having 50% or more identity (e.g., 60, 65, 70, 75, 80, 85, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99.5% or more) to SEQ ID NO:4, 5 or 6. Preferred polypeptides for use may comprise a fragment of at least 8, 9, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more consecutive amino acids of SEQ ID NO:4, 5 or 6. Preferred fragments comprise an epitope from SEQ ID NO: 4, 5 or 6. Other preferred fragments lack one or more amino acids from the N-terminus of SEQ ID NO: 4, 5 or 6 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) and/or one or amino acids from the C-terminus of SEQ ID NO: 4, 5 or 6 while retaining at least one epitope of SEQ ID NO: 4, 5 or 6. Further preferred fragments lack the signal sequence from the N-terminus of SEQ ID NO: 4 or 5. A preferred PhtD polypeptide is SEQ ID NO: 6.

Preferred PhtE polypeptides for use may comprise an amino acid sequence having 50% or more identity (e.g., 60, 65, 70, 75, 80, 85, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99.5% or more) to SEQ ID NO:7 or to SEQ ID NO:8. Preferred polypeptides for use may comprise a fragment of at least 8, 9, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more consecutive amino acids of SEQ ID NO: 7 or 8. Preferred fragments comprise an epitope from SEQ ID NO.7 or to SEQ ID NO: 8. Other preferred fragments lack one or more amino acids from the N-terminus of SEQ ID NO. 7 or 8 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) and/or one or amino acids from the C-terminus of SEQ ID NO:7 or 8 while retaining at least one epitope of SEQ ID NO:7 or 8. Further preferred fragments lack the signal sequence from the N-terminus of SEQ ID NO:7. A preferred PhtE polypeptide is SEQ ID NO:8.

Immunogenic LytB polypeptides include the full length protein with the signal sequence attached, the mature full length protein with the signal peptide removed, variants of LytB (naturally occurring or otherwise, e.g., synthetically derived) and immunogenic fragments of LytB (e.g, fragments comprising at least 15 or 20 contiguous amino acids present in the naturally occurring mature LytB protein). Immunogenic variants and fragments of the immunogenic LytB polypeptides described herein may be capable of eliciting an immune response specific for the corresponding full length mature amino acid sequence. LytB polypeptides suitable for use in the compositions described herein include, for example, those of GenBank Accession Nos. CAA09078, YP816335, ABJ55408, AAK19156, NP358461, and AAK75086, among others.

Preferred LytB polypeptides for use may comprise an amino acid sequence having 50% or more identity (e.g., 60, 65, 70, 75, 80, 85, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99.5% or more) to SEQ ID NO:9, 10 or 11. Preferred polypeptides for use may comprise a fragment of at least, for example, 8, 9, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more consecutive amino acids of SEQ ID NO:9, 10 or 11. Preferred fragments comprise an epitope from SEQ ID NO: 9, 10 or 11. Other preferred fragments lack one or more amino acids from the N-terminus of SEQ ID NO: 9, 10 or 11 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) and/or one or amino acids from the C-terminus of SEQ ID NO:9 or 10 while retaining at least one epitope of SEQ ID NO:9 or 10. Further preferred fragments lack the signal sequence from the N-terminus of SEQ ID NO:10. A preferred LytB polypeptide is SEQ ID NO:11.

(LytB) SEQ ID NO: 9 MKKVRFIFLALLFFLASPEGAMASDGTWQGKQYLKEDGSQAANEWVFDTH YQSWFYIKADANYAENEWLKQGDDYFYLKSGGYMAKSEWVEDKGAFYYLD QDGKMKRNAWVGTSYVGATGAKVIEDWVYDSQYDAWFYIKADGQHAEKEW LQIKGKDYYFKSGGYLLTSQWINQAYVNASGAKVQQGWLFDKQYQSWFYI KENGNYADKEWIFENGHYYYLKSGGYMAANEWIWDKESWFYLKFDGKIAE KEWVYDSHSQAWYYFKSGGYMAANEWIWDKESWFYLKFDGKMAEKEWVYD SHSQAWYYFKSGGYMTANEWIWDKESWFYLKSDGKIAEKEWVYDSHSQAW YYFKSGGYMTANEWIWDKESWFYLKSDGKMAEKEWVYDSHSQAWYYFKSG GYMAKNETVDGYQLGSDGKWLGGKATNKNAAYYQVVPVTANVYDSDGEKL SYISQGSVVWLDKDRKSDDKRLAITISGLSGYMKTEDLQALDASKDFIPY YESDGHRFYHYVAQNASIPVASHLSDMEVGKKYYSADGLHFDGFKLENPF LFKDLTEATNYSAEELDKVFSLLNINNSLLENKGATFKEAEEHYHINALY LLAHSALESNWGRSKIAKDKNNFFGITAYDTTPYLSAKIFDDVDKGILGA TKWIKENYIDRGRTFLGNKASGMNVEYASDPYWGEKIASVMMKINEKLGG KD (LytB) SEQ ID NO: 10 MNLGEFWYNKINKNRGRRLMKKVRFIFLALLFFLASPEGAMASDGTWQGK QYLKEDGSQAANEWVFDTHYQSWFYIKADANYAENEWLKQGDDYFYLKSG GYMAKSEWVEDKGAFYYLDQDGKMKRNAWVGTSYVGATGAKVIEDWVYDS QYDAWFYIKADGQHAEKEWLQIKGKDYYFKSGGYLLTSQWINQAYVNASG AKVQQGWLFDKQYQSWFYIKENGNYADKEWIFENGHYYYLKSGGYMAANE WIWDKESWFYLKFDGKMAEKEWVYDSHSQAWYYFKSGGYMTANEWIWDKE SWFYLKSDGKIAEKEWVYDSHSQAWYYFKSGGYMTANEWIWDKESWFYLK SDGKIAEKEWVYDSHSQAWYYFKSGGYMAKNETVDGYQLGSDGKWLGGKT TNENAAYYQVVPVTANVYDSDGEKLSYISQGSVVWLDKDRKSDDKRLAIT ISGLSGYMKTEDLQALDASKDFIPYYESDGHRFYHYVAQNASIPVASHLS DMEVGKKYYSADGLHFDGFKLENPFLFKDLTEATNYSAEELDKVFSLLNI NNSLLENKGATFKEAEEHYHINALYLLAHSALESNWGRSKIAKDKNNFFG ITAYDTTPYLSAKTFDDVDKGILGATKWIKENYIDRGRTFLGNKASGMNV EYASDPYWGEKIASVMMKINEKLGGKD (LytB construct derived from Spn strain 14453; lacking the signal sequence and choline binding regions; vector derived sequence is underlined) SEQ ID NO: 11 MGKATNENAAYYQVVPVTANVYDSDGEKLSYISQGSVVWLDKDRKSDDKR LAITISGLSGYMKTEDLQALDASKDFIPYYESDGHRFYHYVAQNASIPVA SHLSDMAVGKKYYSADGLHFDGFKLENPFLFKDLTEATNYSAEELDKVFS LLNINNSLLENKGATFKEAEEHYHINALYLLAHSALESNWGRSKIAKDKN NFFGITAYDTTPYLSAKIFDDVDKGILGATKWIKENYIDRGRTFLGNKAS GMNVEYASDPYWGEKIASVMMKINEKLGGKD

Pneumolysin (Ply) is a cytolytic-activating toxin implicated in multiple steps of pneumococcal pathogenesis, including the inhibition of ciliary beating and the disruption of tight junctions between epithelial cells (Hirst et al. Clinical and Experimental Immunology (2004)). Several pneumolysins are known and (following detoxification) would be suitable for use in the compositions described herein including, for example GenBank Accession Nos. Q04IN8, P0C2J9, Q7ZAK5, and AB021381, among others. In one embodiment, Ply has the amino acid sequence shown in SEQ ID NO.12.

Immunogenic pneumolysin polypeptides may include the full length protein with the signal sequence attached, the mature full length protein with the signal peptide removed, variants of pneumolysin (naturally occurring or otherwise, e.g., synthetically derived) and immunogenic fragments of pneumolysin (e.g, fragments comprising at least 15 or 20 contiguous amino acids present in the naturally occurring mature pneumolysin protein). Immunogenic variants and fragments of the immunogenic pneumolysin polypeptides may be capable of eliciting an immune response specific for the corresponding full length mature amino acid sequence. The immunogenic pneumolysin polypeptides are typically detoxified; that is, they lack or have reduced toxicity as compared to the mature wild-type pneumolysin protein produced and released by S. pneumoniae. The immunogenic pneumolysin polypeptides may be detoxified for example, chemically (e.g., using formaldehyde treatment) or genetically (e.g., recombinantly produced in a mutated form). Preferred examples of the immunogenic detoxified pneumolysin are disclosed in PCT Publication No. WO 2010/071986. In one embodiment, immunogenic detoxified pneumolysin has the amino acid sequence shown in SEQ ID NO: 13.

Preferred pneumoysin polypeptides may comprise an amino acid sequence having 50% or more identity (e.g., 60, 65, 70, 75, 80, 85, 85, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 99.5% or more) to SEQ ID NO:12 or to SEQ ID NO:13. Preferred polypeptides may comprise a fragment of at least 8, 9, 10, 12, 14, 16, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250 or more consecutive amino acids of SEQ ID NO:12 or 13. Preferred fragments may comprise an epitope from SEQ ID NO:12 or to SEQ ID NO:13. Other preferred fragments lack one or more amino acids from the N-terminus of SEQ ID NO. 12 or 13 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25 or more) and/or one or amino acids from the C-terminus of SEQ ID NO:12 or 13 while retaining at least one epitope of SEQ ID NO:12 or 13. Further preferred fragments lack the signal sequence from the N-terminus of SEQ ID NO:12. A preferred immunogenic and detoxified pneumolysin polypeptide is SEQ ID NO:13.

(PLY) SEQ ID NO: 12 MANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKK RSLSINTSDISVTATNDSRLYPGALLVVDETLLENNPILLAVDRAPMTYS IDLPGLASSDSFLQVEDPSNSSVRGAVNDLLAKWHQDYGQVNNVPARMQY EKITAHSMEQLKVKFGSDFEKTGNSLDIDFNSVHSGEKQIQIVNFKQIYY TVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSVAYGRQVYLKL ETTSKSDEVEAAFEALIKGVKVAPQTEWKQILDNTEVKAVILGGDPSSGA RVVTGKVDMVEDLIQEGSRFTADHPGLPISYTTSFLRDNVVATFQNSTDY VETKVTAYRNGDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRN GQDLTAHFTTSIPLKGNVRNLSVKIRECTGLATNETNTNRIVYEKTDLPL VRKRTISITNGTTLYPQVEDKVEND (PlyD1 construct derived from Spn strain 14453) SEQ ID NO: 13 MANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKK RSLSINTSDISVTACNDSRLYPGALLVVDETLLENNPILLAVDRAPMTYS IDLPGLASSDSFLQVEDPSNSSVRGAVNDLLAKWHQDYGQVNNYPARMQY EKITAHSMEQLKVKFGSDFEKTGNSLDIDFNSVHSGEKQIQIVNFKQIYY TVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSVAYGRQVYLKL ETTSKSDEVEAAFEALIKGVKVAPQTEWKQILDNTEVKAVILCGDPSSGA RVVTGKVDMVEDLIQEGSRFTADHPGLPISYTTSFLRDNVVATFQNSTDY VETKVTAYRNGDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRN GQDLTAHFTTSIPLKGNVRNLSVKIREATGLATNETNTNRIVYEKTDLPL VRKRTISITNGTTLYPQVEDKVEND

Variants of the immunogenic polypeptides described herein are selected for their immunogenic capacity using methods well known in the art. Such variants may comprise amino acid modifications. For example, amino acid sequence modifications include substitutional, insertional or deletional changes. Substitutions, deletions, insertions or any combination thereof may be combined in a single variant so long as the variant is an immunogenic polypeptide. Insertions include amino and/or carboxyl terminal fusions as well as intrasequence insertions of single or multiple amino acid residues. Insertions ordinarily will be smaller insertions than those of amino or carboxyl terminal fusions, for example, on the order of one to four residues. Deletions are characterized by the removal of one or more amino acid residues from the protein sequence. Typically no more than about from 2 to 6 residues are deleted at any one site within the protein molecule. These variants ordinarily are prepared by site specific mutagenesis of nucleotides in the DNA encoding the protein, thereby producing DNA encoding the variant, and thereafter expressing the DNA in a recombinant cell culture. Techniques for making substitution mutations at predetermined sites in DNA having a known sequence are well known and include, but are not limited to, M13 primer mutagenesis and PCR mutagenesis. Amino acid substitutions are typically of single residues but can occur at a number of different locations at once. Substitutional variants are those in which at least one residue has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the following Table and are referred to as conservative substitutions. Others are well known to those of skill in the art.

As used herein, the amino acid substitution may be conservative or non-conservative. Conservative amino acid substitutions may involve a substitution of a native amino acid residue with a non-native residue such that there is little or no effect on the size, polarity, charge, hydrophobicity, or hydrophilicity of the amino acid residue at that position and, in particular, does not result in decreased immunogenicity. Suitable conservative amino acid substitutions are shown in the Table 1 below.

TABLE 1 Preferred Original Conservative Residues Exemplary Conservative Substitutions Substitution Ala Val, Leu, Ile Val Arg Lys, Gln, Asn Lys Asn Gln Gln Asp Glu Glu Cys Ser, Ala Ser Gln Asn Asn Glu Asp Asp Gly Pro, Ala Ala His Asn, Gln, Lys, Arg Arg Ile Leu, Val, Met, Ala, Phe, Norleucine Leu Leu Norleucine, Ile, Val, Met, Ala, Phe Ile Lys Arg, 1,4 Diamino-butyric Acid, Gln, Asn Arg Met Leu, Phe, Ile Leu Phe Leu, Val, Ile, Ala, Tyr Leu Pro Ala Gly Ser Thr, Ala, Cys Thr Thr Ser Ser Trp Tyr, Phe Tyr Tyr Trp, Phe, Thr, Ser Phe Val Ile, Met, Leu, Phe, Ala, Norleucine Leu

A skilled artisan will be able to determine suitable variants of the polypeptides and/or fragments provided herein using well-known techniques.

Analogs can differ from naturally occurring S. pneumoniae polypeptides in amino acid sequence and/or by virtue of non-sequence modifications. Non-sequence modifications include changes in acetylation, methylation, phosphyorylation, carboxylation, or glycosylation. A “modification” of a polypeptide may include polypeptides (or analogs thereof, such as, e.g. fragments thereof) that are chemically or enzymatically derived at one or more constituent amino acid. Such modifications can include, for example, side chain modifications, backbone modifications, and N- and C-terminal modifications such as, for example, acetylation, hydroxylation, methylation, amidation, and the attachment of carbonhydrate or lipid moieties, cofactors, and the like, and combinations thereof. Modified polypeptides described herein may retain the biological activity of the unmodified polypeptides or may exhibit a reduced or increased biological activity.

Structural similarity of two polypeptides can be determined by aligning the residues of the two polypeptides (for example, a candidate polypeptide and the polypeptide of, for example, SEQ ID NO: 2) to optimize the number of identical amino acids along the length of their sequences; gaps in either or both sequences are permitted in making the alignment in order to optimize the number of identical amino acids, although the amino acids in each sequence must nonetheless remain in their proper order. A candidate polypeptide is the polypeptide being compared to the reference polypeptide. A candidate polypeptide can be isolated, for example, from a microbe, or can be produced using a recombinant techniques, or chemically or enzymatically synthesized.

A pair-wise comparison analysis of amino acids sequences can be carried out using a global algorithm, for example, Needleman-Wunsch. Alternatively, polypeptides may be compared using a local alignment algorithm such as the Blastp program of the BLAST 2 search algorithm, as described by Tatiana et al., (FEMS Microbiol. Lett, 174 247-250 (1999), and available on the National Centre for Biotechnology Information (NCBI) website. The default values for all BLAST 2 search parameters may be used, including matrix=BLOSUM62; open gap penalty=11, extension gap penalty=1, gap×dropoff=50, expect 10, wordsize=3, and filter on. The Smith and Waterman algorithm is another local alignment tool that can be used (1988).

In the comparison of two amino acid sequences, structural similarly may be referred to by percent “identity” or may be referred to by percent “similarity.” “Identity” refers to the presence of identical amino acids. “Similarity” refers to the presences of not only identical amino acid but also the presence of conservative substitutions. A conservative substitution for an amino acid in a polypeptide described herein may be selected from other members of the class to which the amino acid belongs, shown on Table 1.

Compositions

Compositions (e.g., vaccine compositions) may be administered in the presence or absence of an adjuvant. Adjuvants generally are substances that can enhance the immunogenicity of antigens. Adjuvants may play a role in both acquired and innate immunity (e.g., toll-like receptors) and may function in a variety of ways, not all of which are understood.

Many substances, both natural and synthetic, have been shown to function as adjuvants. For example, adjuvants may include, but are not limited to, mineral salts, squalene mixtures, muramyl peptide, saponin derivatives, mycobacterium cell wall preparations, certain emulsions, monophosphoryl lipid A, mycolic acid derivatives, nonionic block copolymer surfactants, Quil A, cholera toxin B subunit, polyphosphazene and derivatives, immunostimulating complexes (ISCOMs), cytokine adjuvants, MF59 adjuvant, lipid adjuvants, mucosal adjuvants, certain bacterial exotoxins and other components, certain oligonucleotides, PLG, and others. These adjuvants may be used in the compositions and methods described herein.

In certain embodiments, the composition is administered in the presence of an adjuvant that comprises an oil-in-water emulsion comprising at least squalene, an aqueous solvent, a polyoxyethylene alkyl ether hydrophilic nonionic surfactant, a hydrophobic nonionic surfactant, wherein said oil-in-water emulsion is obtainable by a phase inversion temperature process and wherein 90% of the population by volume of the oil drops has a size less than 200 nm, and optionally less than 150 nm. Such an adjuvant is described in WO2007006939 (Vaccine Composition Comprising a Thermoinversable Emulsion) which is incorporate herein in its entirety. The composition may also include the product E6020 (having CAS Number 287180-63-6), in addition to, or instead of the described squalene oil-in-water emulsion. Product E6020 is described in US2007/0082875 (which is incorporated herein by reference in its entirety).

In certain embodiments, the composition includes a TLR agonist (e.g., TLR4 agonist) alone or together in combination with an adjuvant. For example, the adjuvant may comprise a TLR4 agonist (e.g., TLA4), squalene, an aqueous solvent, a nonionic hydrophilic surfactant belonging to the polyoxyethylene alkyl ether chemical group, a nonionic hydrophobic surfactant and which is thermoreversible. Examples of such adjuvants are described in WO2007080308 (Thermoreversible Oil-in-Water Emulsion) which is incorporated herein in its entirety. In one embodiment, the composition is adjuvanted with a combination of CpG and an aluminum salt adjuvant (e.g., Alum).

Aluminum salt adjuvants (or compounds) are among the adjuvants of use in the practice described herein. Examples of aluminum salt adjuvants of use include aluminum hydroxide (e.g., crystalline aluminum oxyhydroxide AlO(OH), and aluminum hydroxide Al(OH)₃. Aluminum hydroxide is an aluminum compound comprising Al³⁺ ions and hydroxyl groups (—OH). Mixtures of aluminum hydroxide with other aluminum compounds (e.g., hydroxyphosphate or hydroxysulfate) may also be of use where the resulting mixture is an aluminum compound comprising hydroxyl groups. In particular embodiments, the aluminum adjuvant is aluminum oxyhydroxide (e.g., Alhydrogel®). It is well known in the art that compositions with aluminum salt adjuvants should not be exposed to extreme temperatures, i.e. below freezing (0° C.) or extreme heat (e.g., ≥70° C.) as such exposure may adversely affect the stability and the immunogenicity of both the adsorbed antigen and adjuvant.

In a particular embodiment, the aluminum compound (e.g., aluminum hydroxide adjuvant) is treated with phosphate

In a preferred embodiment, phosphate is added to aluminum hydroxide adjuvant in the form of a salt. Preferably, the phosphate ions are provided by a buffer solution comprising disodium monosodium phosphate.

In a preferred practice, as exemplified herein, the aluminum compound (e.g., aluminum oxyhydroxide) is treated with phosphate (for example, by a process as described in WO2011/075822 (filed on 20 Dec. 2010 and entitled, Immunogenic Compositions and Related Methods). In this process, an aqueous suspension of aluminum oxyhydroxide (approximately 20 mg/mL) is mixed with a phosphate buffer solution (e.g., approximately 400 mol/L). The preferable final phosphate concentration is from about 2 mM to 20 mM. The mixture is then diluted with a buffer (e.g., Tris-HCl, Tris-HCl with saline, HEPES) to prepare a suspension of aluminum oxyhydroxide and phosphate (PO4). Preferably the buffer is 10 mM Tris-HCl and 150 mM NaCl at a pH of about 7.4. The suspension is then mixed for approximately 24 hr at room temperature. Preferably the concentration of elemental aluminum in the final suspension is within a range from about 0.28 mg/mL to 1.68 mg/mL. More preferably, the concentration of elemental aluminum is about 0.56 mg/mL.

The immunogenic polypeptides (e.g., PcpA, PhtD), individually or in combination may then be adsorbed to the treated aluminum hydroxide.

The compositions may preferably be in liquid form, but they may be lyophilized (as per standard methods) or foam dried (as described in WO2009012601, Antigen-Adjuvant Compositions and Methods). A composition according to one embodiment is in a liquid form. An immunization dose may be formulated in a volume of between 0.5 and 1.0 ml. Liquid formulations may be in any form suitable for administration including for example, a solution, or suspension. Thus, the compositions can include a liquid medium (e.g., saline or water), which may be buffered.

The pH of the formulation (and composition) may preferably be between about 6.4 and about 8.4. More preferably, the pH is about 7.4. An exemplary pH range of the compositions is 5-10, e.g., 5-9, 5-8, 5.5-9, 6-7.5, or 6.5-7. The pH may be maintained by the use of a buffer.

The pharmaceutical formulations of the immunogenic compositions may also optionally include one or more excipients (e.g., diluents, thickeners, buffers, preservatives, surface active agents, adjuvants, detergents and/or immunostimulants) which are well known in the art. Suitable excipients will be compatible with the antigen(s) and with the adjuvant as is known in the art. Examples of diluents include binder, disintegrants, or dispersants such as starch, cellulose derivatives, phenol, polyethylene glycol, propylene glycol or glycerin. Pharmaceutical formulations may also include one or more active ingredients such as antimicrobial agents, anti-inflammatory agents and anesthetics. Examples of detergents include a Tween (polysorbate) such as Tween 80. Suitable excipients for inclusion in the composition are known in the art.

In one embodiment of adjuvanted immunization, for example, immunogenic polypeptides and/or fragments thereof may be covalently coupled to bacterial polysaccharides to form polysaccharide conjugates. Such conjugates may be useful as immunogens for eliciting a T cell dependent immunogenic response directed against the bacterial polysaccharide conjugated to the polypeptides and/or fragments thereof.

Immunogenic compositions may be presented in a kit form comprising the immunogenic composition and an adjuvant or a reconstitution solution comprising one or more pharmaceutically acceptable diluents to facilitate reconstitution of the composition for administration to a mammal using conventional or other devices. Such a kit would optionally include the device for administration of the liquid form of the composition (e.g. hypodermic syringe, microneedle array) and/or instructions for use.

EXAMPLES

The above disclosure generally describes certain embodiments of this subject matter. A more complete understanding can be obtained by reference to the following specific Examples. These Examples are described solely for purposes of illustration and are not intended to limit the scope of this disclosure. Changes in form and substitution of equivalents are contemplated as circumstances may suggest or render expedient. Although specific terms have been employed herein, such terms are intended in a descriptive sense and not for purposes of limitations.

Methods of molecular genetics, protein biochemistry, and immunology used, but not explicitly described in this disclosure and these Examples, are amply reported in the scientific literatures and are well within the ability of those skilled in the art.

Immune Responses

CD4+ T-cells are considered of prime importance against extracellular pathogens such as for example, S. pneumonaie. Upon stimulation with antigen loaded antigen-presenting cells (APCs) in context to MHC class II molecules, naïve CD4+ T-cells may differentiate into functionally different T-helper (Th)-subsets. The commitment to different Th-subsets depends on a complex interaction with APCs in a permissive milieu, including antigenic type and load, co-stimulatory molecules and cytokine signaling (7-9). For example, Th1 cells, characterized by interleukin (IL)-2, interferon-gamma (IFN-γ) and tumor necrosis factor-beta (TNF-β), production are of primary importance to eradicate intracellular pathogens. Th2-cells, essential in eliminating extracellular pathogens, express IL-4, IL-5, IL-6, IL-10, IL-13, and IL-25. Recently discovered Th17 cells secrete IL-17, IL-21, and IL-22 (10).

Memory T-cell responses are either generated during the effector response (linear model or asymmetric division) or are the remnant of a large cache of effector clonotypes that contracts and persists after pathogen clearance (11). Immunological memory, with its rapid recall responses and high cytokine production represents a highly effective mechanism to ensure quick protection against prevalent infection, and serves as a primary defense against pathogen re-encounter at portal entry points such as the respiratory mucosa (12; 13). Robust memory T- and B-cell responses are generated during both onset of a natural infection as well as upon vaccination, with memory lymphocytes populating lymphoid and non-lymphoid sites (14-16). Once generated, memory T-cells can be detected in the blood circulation over a period of time (15; 17; 18). Current concepts of generating immunity against Spn have evolved from studies in mice defining a major role for CD4+ Th (helper)-memory subsets (Th-1, Th-2 & Th-17) (19-21). In animal models CD4+ T-cell immunity plays a significant role in protection against otopathogens and can also impart antibody independent immunity (20; 22; 23). However, there is no data to support a protective role of T-helper memory subsets among humans experiencing AOM.

The central role of antigen specific CD4+ T-cells in the adaptive immune response is to provide help for B-cells in the production of antibodies on the one hand and as their own effectors of immune function on the other (7; 9; 23; 27). Furthermore, in the constant cytokine milieu provided by Th-cells and in response to antigenic stimulation, specific B-cells undergo clonal expansion, class switch and somatic hyper mutation leading to the selection of antibodies with higher affinity (28; 29). The expanded B-cells differentiate into plasma cells that secret antibodies at high rate and persist in niches like bone marrow while some differentiate into memory B-cells (29; 30). The memory B-cells can rapidly respond to antigenic re-stimulation and may contribute to maintain the plasma cell pool and therefore serum antibody levels for prolonged periods of time with the constant help from CD4+ T-cells (31).

Example 1

To evaluate the otitis-prone condition in children, using pneumococcal protein antigens, Spn specific functional memory CD4+ Th-cell subsets in the peripheral blood of a cohort of non otitis-prone and otitis-prone children were enumerated. The B-cell IgG responses were also measured to the same antigens in the serum of the children of these cohorts.

Subjects were participants from a 5-year prospective longitudinal AOM study funded by the US NIH (26). Children having three episodes of AOM within 6 months or 4 episodes within one year were considered as otitis-prone while others who had fewer episodes were placed into the non otitis-prone group. Enrolled children were from a middle class, suburban socio-demographic population in Rochester N.Y. Healthy children at age of 6 months without prior AOM were enrolled and had serum, nasopharyngeal (NP) and oropharyngeal (OP) cultures obtained seven times, at the age 6, 9, 12, 15, 18, 24 and 30 months and both the cohorts had children of varying age under 2 yr. Middle ear fluid was obtained by tympanocentesis during AOM episodes. Evaluation of NP/OP colonization with Streptococcus pneumoniae and Haemophilus influenzae) was routinely obtained by microbiological tests of the cultured NP and OP surface and middle ear fluids. PBMCs from the collected blood were isolated and frozen in the liquid nitrogen until used. Samples used in this study were taken at the time of their AOM visits from otitis-prone children, and during colonization or AOM visits from non otitis-prone group. Children had been immunized against S. pneumoniae according to applicable schedule with age appropriate doses of available conjugate vaccine.

Antigens

Pneumococcal protein antigens used were PhtD (SEQ ID NO:6), PhtE (SEQ ID NO:8), LytB (SEQ ID NO:11), PcpA (SEQ ID NO:3), and PlyD1 (SEQ ID NO:13), a detoxified derivative of pneumolysin. As a control, PspA was also used. Each of the proteins were cloned from a S. pneumoniae serotype 6B strain and recombinantly expressed in E. coli as soluble proteins and then purified with combinations of ion exchange chromatography. The proteins each had ≥90% purity after purification as assayed by SDS-PAGE and RP-HPLC.

An optimal dosage for stimulation was determined by absence of detectable cell toxicity, by the use of tryptan blue staining and/or flow cytometry analysis after propidium iodide staining (data not shown).

T-Cell Stimulation

PBMCs from otitis prone and non-otitis prone children who were NP colonized or AOM-infected with Spn were stimulated with the six pneumococcal antigens whereas children who were NP colonized or AOM-infected with NTHi were stimulated with the three NTHi antigens. Prior to stimulation, frozen PBMCs were quickly thawed in a 37° C. water bath followed by slowly adding complete culture medium (RPMI 1640 supplemented with 10% of FBS, 2 mM L-glutamine, 0.1 mM sodium pyruvate, nonessential amino acids, 100 U/mL penicillin, 100 μg/mL streptomycin). Cells were then washed and rested overnight in complete culture media in 24-well plates. PBMCs were stimulated using a standardized protocol adapted from previous reports (35; 36). Briefly, cells were counted and placed in a 96-well flat bottom culture plate and were stimulated with either 1 μg/ml of various protein antigens or with 1 μg/ml of Staphylococcal enterotoxin B (SEB). To the cell culture 1 μg/ml concentrations of anti-CD28 and anti-CD49d antibodies (clones L293 and L25 respectively; BD Biosciences) were added to provide co-stimulation and enhance the detection of antigen specific responses. Anti-CD28 and CD49d antibodies have been widely used for co-stimulation without affecting background levels (18; 37). Cells were then incubated for 2 h at 37° C. in the presence of 5% CO₂ for antigen processing. After 2 hours, golgi transport inhibitors (BD Biosciences) were added to preserve cytokines intracellularly and incubation was then continued for an additional 4 hours.

Cytokine Profiling

A multi-parameter flow cytometry approach was used to detect specific CD4+ T-cell responses to the Spn proteins in the circulation after AOM or NP colonization in study cohorts. An intracellular cytokine staining assay (ICCS) was used to evaluate antigen specific CD4+ T-cell subsets (Th-1, Th-2 and Th-17). After stimulation, cells were transferred to 96-well V-bottom plates and washed once with FACS buffer (PBS with 5% FBS) and stained with the antibodies to various cell surface markers. Antibodies used were anti-CD4 APC Alexafluor 750 (clone RPA T4, eBiosciences), PE-Texas Red anti-CD45RA (clone MEM56, Invitrogen), anti-CCR7 PerCP/Cy5.5 conjugate (clone TG8/CCR7, Biolegend). Cells were then permeabilized with fixation and permeabilization solution (BD Biosciences) for 20-minutes and washed three times with 1× permeabilization buffer (BD Biosciences). A cocktail of various cytokine specific antibodies was used to stain intracellularly captured cytokines as a result of stimulation. Antibodies used were PE-Cy7 conjugated anti-IFN-γ (clone B27, BD biosciences), Pacific blue conjugated anti IL17A (clone BL168, Biolegend), Alexa fluor 700 anti IL-2 (clone MQ1-17H12, Biolegend), PE conjugated anti IL-4 (clone 8D4-8, BD Biosciences), AF 488 conjugated TNF-α, anti-CD3 Qdot 605 (clone UCHT1, Invitrogen) and PE-Cy5 anti-CD69 (clone FN50, BD biosciences). After intracellular staining, cells were further washed 3-times with 1× permeabilization buffer and one final wash with FACS buffer before resuspending them into the FACS tubes. A custom made BD LSR II flow cytometer equipped for the detection of 12 fluorescent parameters was used to collect 2-5×105 events for each sample and data was analyzed using FLOW JO (Tree Star) software. To exclude cell debris and clumps, cells were first gated based on their forward- and side-scatter properties followed by sequential gating on CD4+ T-cells followed by CD45RALow and then to CD69+ cytokine positive cells. Alternatively, cells were also gated on TNF-α Vs other cytokines for confirmation. Low frequency responders were confirmed by excessive back gating. As previously reported, to aid in the detection of antigen specific cells anti-CD28/CD49d antibodies in conjunction with multi-parameter staining was used to help avoid irrelevant background (37). The whole assay was standardized and compared to multiplex bead array (CBA, BD Biosciences) for the detection of cytokine profile.

Humoral Responses

For measuring IgG antibody levels in the samples, ELISA was performed as described earlier (26; 38). Briefly, 96-well plates (Nunc-Immulon) were coated with 0.25 μg/ml of individual antigens (100 μl/well) in coating buffer (bicarbonate, (pH 9.4) and incubated overnight at 4° C. After washing the plates were blocked with 3% skimmed milk at 37° C. for 1 hr (200 μl per well). After five washes, 100 μl of serum at a starting dilution of 1:100 (in PBS-3% skim milk) was added to the wells and diluted serially 2 fold. The mixture was incubated at room temperature for 1 hr followed by the addition of affinity purified goat anti-human IgG antibody conjugated to horseradish-peroxidase (Bethyl Laboratories, Inc, Montgomery, Tex.) as a secondary antibody. The reaction products were developed with TMB Microwell Peroxidase Substrate System (KPL, Gaithersburg, Md.), stopped by the addition of 1.0 molar phosphoric acid and read by an automated ELISA reader using a 450-nm filter. To provide quantitative results on antibody concentrations, the level of the specific antibody present in the unknown sample was determined by comparison to an internal reference serum (pool of human serum with high antigen specific antibody levels). The levels of IgG in the reference serum were quantitatively measured by using a human IgG ELISA quantitation kit (Bethyl laboratories). A Four-parameter logistic-log function was used to form the reference and sample curves. This ELISA was fully validated according to ICH Guidance.

All data was statistically analyzed using Graph Pad Prism software. Two tailed P values for the data were calculated using Mann Whitney Test.

Results

Children in the otitis prone group were of a similar age as the non-otitis prone children. The distribution in gender, day care attendance, passive cigarette smoke exposure in the household, number of siblings under 8 years of age and breast fed were similar in the two study groups.

The circulating frequencies of various Spn antigen specific memory Th-cell subsets were compared between non otitis-prone and otitis-prone children by stimulating their PBMCs with specific antigens. For that, the percentages of CD45RALow memory CD4+ T-cells producing IFN-γ, IL-4, IL-2 or IL-17 were calculated by gating on recently activated CD69+ T-cells. Antigen specific responses were normalized with the control PBMCs left unstimulated or stimulated with a non specific antigen (Keyhole limpet hemocyanin).

FIG. 1, which sets out a summary of the results, demonstrates detectable frequencies of the various subsets of CD45RALow memory CD4+ T-cells to all the Spn antigens used for stimulation in non otitis prone children (n=15) following AOM (n=6) or NP colonization (n=9) with Spn. In sharp contrast, otitis-prone children (n=13) had a marked deficiency of circulating Spn specific memory CD4+ T-cells after AOM (n=10) and NP colonization (n=3). In particular, there was a complete lack of memory CD4+ T-cells producing IFN-γ against LytB, PhtE and Ply whereas significantly lower levels of IFN-γ were produced in response to PhtD, PcpA and PspA (P<0.02) (FIG. 1a ). A significant decrease in IL-4 producing memory CD4+ T-cells was observed against PhtD and LytB (P<0.02) in the otitis-prone children (FIG. 1b ). IL-2 responses to PhtD (P<0.05), PcpA (P<0.005), PhtE (P<0.05), Ply (P<0.005) and PspA (0.02) were significantly lower in otitis-prone children (FIG. 1c ) and a significant reduction in IL-17a producing cells were found in otitis-prone children in response to PhtD, PcpA and PhtE (P<0.05) (FIG. 1d ).

As the absence of antigen specific memory Th-cells may result in impaired antigen specific B-cell responses (9), the antigen specific IgG titers in the non otitis-prone and otitis-prone children were assessed. Serum IgG levels against the pneumococcal antigens in the respective groups are shown in FIG. 2. As expected, with the increased memory T-cell frequencies, IgG titers to PhtD, LytB, PhtE, Ply were significantly higher in the non otitis-prone group compared to otitis-prone group (P<0.05; 0.0005; 0.0005; 0.005 respectively) (FIG. 2). There was an increase in the IgG titer to PcpA antigen as well but the difference was not significant (FIG. 3).

Since, the immune system in young children is not fully mature in the context of T- and B-cell responses (39; 40), B cell and T cell mediated responses were tested to assess whether the whether the impaired memory T-cell responses among otitis-prone children were due to intrinsic T- or B-cell defects. PBMC were stimulated with SEB, an antigen that stimulates a T-cell response independent of APC involvement (41). FIG. 3 shows the percentage of memory CD4+ T-cells producing IFN-γ, IL-4, IL-2 or IL-17a is the same for otitis prone and non otitis prone children. Given that all the children had received a DTaP vaccine, IgG titers against the vaccine antigens diphtheria, tetanus and pertussis were determined to assess whether the otitis prone child has a generalized immune deficiency. No significant differences were found in IgG antibody concentrations to diptheria toxoid, tetanus toxoid, pertussis toxin, filamentous hemagglutinin or pertactin between the groups (data not shown).

In sum, these data show that Spn otitis-prone children have a lack or reduction of pneumococcal antigen specific functional memory CD4+ T-cells as compared to non-otitis prone children. This effect was associated with reduced IgG responses to the studied antigens. As shown by the data, otitis-prone children fail to generate antigen specific CD45RALow functional Th-memory responses to Spn and elicit reduced antibody responses to Spn protein antigens. These children are not however deficient in total functional memory T-cells or in eliciting B cell mediated antibody responses (e.g., IgG) against vaccinated antigens.

In spite of the fact that CD4+ Th cells assist in fighting infections caused by Spn and NTHi, there has not been any previous report demonstrating a direct role of specific CD4+ Th-cells associated with Spn or NTHi-mediated AOM in children. Clearly, poor generation of CD4+ T-cell memory in children would lead to subsequent diminished B-cell mediated antibody responses. The lack of immunologic memory thus could result in repeated susceptibility to recurrent ear infections. Here, for the first time we demonstrate that otitis-prone children have an absence/reduction in otopathogen (e.g., S. pneumoniae) specific memory among Th-cells in the blood circulation following AOM and/or NP colonization. In contrast, non otitis-prone children generate memory antigen specific CD4+ T-cells after AOM and/or NP colonization with otopathogens.

It appears that the otitis prone child does develop a short-lived B cell response since some antibodies are detectable among these children after AOM and NP colonization with S. pnuemoniae. However, in the absence of T cell memory, after the antibody level wanes the child quickly becomes susceptible to additional AOM infections. Thus, the fundamental immunologic deficit appears to be in the generation of T cell memory among otitis prone children. Since otitis-prone children responded similarly to an antigen that does not require APC processing (SEB) and similarly to a parenteral injection of antigen in the form of a DTaP vaccine, it may be that the problem among otitis prone children lays even further upstream immunologically in the actual processing and presentation of Spn and NTHi antigens by APCs present in the nasal mucosa.

Previous work has demonstrated the role of Spn and NTHi antigens in CD4+ T-cell proliferative responses (for 5-7 days) among children and adults (42; 43). A prior study evaluated CD4+ T-cell proliferation from cells collected from the adenoids and tonsils of otitis-prone children and found no proliferation in response to NTHi protein P6 (44). Studies of this nature evaluate antigen specific T-cell proliferation but fail to inform about occurrence of antigen specific memory CD4+ T-cells.

While CD4+ Th-2 cells promote most of the antibody responses that help in the elimination of bacterial pathogens from the host, recent studies in mouse models have shown antibody independent immunity to Spn NP colonization mediated by IL-17a producing CD4+ T-cells (Th-17 cells)(20). Here for the first time, in humans, increased frequencies were detected of Spn-specific IL-17a producing memory Th-cells in the circulation of non otitis-prone children, as compared to otitis-prone children. Thus, Spn-specific IL-17a producing memory Th-cells may protect against the otitis-prone condition.

The cellular phenotyping at the site of infection during AOM (middle ear mucosa and middle ear fluid) suggests a large migration of CD45ROHigh/CD45RALow memory CD4+ T-cells with loss of homing receptors L-selectin (45). Other studies reveal accumulation of mainly memory CD4+ T-cells in the middle ear fluid during AOM (45-47). Local secondary lymphoid organs such as adenoids are the primary sites for T-cell priming during upper respiratory tract infections such as bacterial colonization. Once, an antigen loaded APC migrates to local lymphoid organs (adenoids), the differentiation of lymphocytes (c.f. CD4+ T-cells) takes place. After entering the blood circulation the CD4+ T-cells eventually migrate to the middle ear mucosa (in the case of AOM) and/or the upper respiratory tract (during NP colonization).

Without being bound by theory, delayed immunologic maturation likely is responsible for the lack of functional T-cells among otitis-prone children (48). As children age, they become less prone to AOM because of anatomical changes in the eustachion tube but also with age maturation of the immune system occurs. A robust T-cell memory response typically develops around age 3 to 5 years (40; 48-51), and usually the otitis prone child “outgrows” their propensity during this age time frame.

In humans, memory CD4+ T-cells may play a key role in the fight against AOM. Therefore, Spn specific CD4+ T-cell memory, if generated, would be useful in the prevention of recurrent AOM incidences.

Example 2

In this study, the development of serum IgG antibodies to PhtD, PhtE, LytB, PcpA and Ply among three groups of 6 to 36 month old children with AOM were compared: 1) an otitis prone group that included children who had three or more episodes of AOM in six months or four or more episodes in a 12 month period; 2) an AOM treatment failure (AOMTF) group that included children who failed to achieve bacterial eradication and/or resolution of symptoms after at least 48 hours of appropriate antibiotic therapy (70; 71) and children whose signs and symptoms of AOM returned within 14 days of completing an antibiotic treatment course; and, 3) a non-otitis prone group that included children who had only one or two episodes of AOM.

The samples collected and analyzed were obtained during the prospective study referenced in Example 1. Healthy children without prior AOM were enrolled at age 6 months and followed prospectively until 30 months of age. Serum, NP and oropharyngeal (OP) cultures were obtained seven times during the study period at age 6, 9, 12, 15, 18, 24, and 30 months. However, samples for the 30 month time point were excluded from this analysis as too few subjects had reached the 30 month visit. During the study period whenever a child experienced an AOM, serum, NP and OP cultures were obtained along with middle ear fluid (MEF) by tympanocentesis. Convalescent samples were collected three weeks later. The majority of these children developed no AOMs (about 70%) and were included in group 3 (non-otitis prone children). Some children went on to meet the definitions of otitis-prone (about 5%) and were included in group 1 or had AOMTF (about 5%) and were included as group 2 for analysis. To increase the size of the otitis prone and AOMTF cohorts, additional children were enrolled whenever they met those definitions within the age time span of 6 to 36 months old. At the time of an AOM event, serum, NP, OP and MEF samples were collected acutely; and convalescent samples 3 weeks later.

To assure the diagnosis of AOM, children were examined by validated otoscopist pediatricians using the American Academy of Pediatrics AOM diagnostic guidelines. A tympanocentesis was performed to confirm the presence of an otopathogen in MEF. MEF, NP, and OP samples were inoculated into trypticase soy broth, trypticase soy agar with 5% sheep blood plates, and chocolate agar plates. Bacteria were isolated according to the CLSI standard culture procedures.

ELISA assay: The S. pneumoniae proteins PhtD, LytB, PcpA, PhtE and PlyD1 used in Example 1 were also used in this study. Protein specific antibody titers were determined by ELISA using purified recombinant proteins. 96-well Nunc-Immulon 4 plates were coated with 0.5 μg/ml of individual proteins (1000/well) in bicarbonate coating buffer (pH 9.4) and incubated overnight at 4° C. After washing the plates were blocked with 3% skim milk at 37° C. for 1 hr (200 μl per well). After five washes, 100 μl of serum at a starting dilution of 1:100 (in PBS-3% skim milk) was added to the wells and diluted serially 2 fold. The mixture was incubated at room temperature for 1 hr followed by the addition of affinity purified goat anti-human IgG antibody conjugated to horseradish-peroxidase (Bethyl Laboratories, Inc, Montgomery, Tex.) as a secondary antibody. The reaction products were developed with TMB Microwell Peroxidase Substrate System (KPL, Gaithersburg, Md.), stopped by the addition of 1.0 molar phosphoric acid and The plates were analyzed at 450 nm on a Spectra max plate reader (Molecular Devices, Sunnyvale, Calif.) using the Softmax endpoint dilution protocol.

Statistical analysis was performed on GraphPad Prism 5. Unpaired t test was used to compare the difference among three groups for the IgG antibody analysis. Paired t test was applied to compare acute vs. convalescence serum samples. One way ANOVA was used to evaluate the antibody rise over time. P values of <0.05 were considered significant.

Specific IgG Antibody Titers Against PhtD, LytB, PcpA, PhtE and Ply in Three Groups of Children at the Time of an AOM

IgG antibody titers against PhtD, LytB, PcpA, PhtE and Ply proteins of Spn were measured at the time of an acute AOM in 35 otitis prone children, 25 children with AOMTF and 34 children with their first or second AOM as a non-otitis prone group (FIG. 4).

The IgG titers against protein PhtD in the otitis prone children were significantly lower compared to non-otitis-prone children (p<0.05). The IgG antibody levels to PhtD in AOMTF children were also lower compared to non otitis-prone children but the difference did not achieve significance. The IgG titers to LytB in the otitis prone children and AOMTF children were significantly lower compared to non-otitis prone children (p<0.001 for both comparisons). The GMTs of IgG against protein PcpA in the otitis prone and AOMTF children were almost 3 times lower compared to non-otitis prone children but the difference was not statistically significant among 3 groups of children due to wide variation in levels of antibody. The IgG titers to protein PhtE in the otitis-prone children and AOMTF children were significantly lower compared to non-otitis prone children (p<0.001). The IgG titers to protein PlyD1 were significantly lower in the otitis prone children (p=0.006) and AOMTF children (p=0.02) compared to non-otitis prone children.

Acute and Convalescent AOM Antibody Levels Against PhtD, LytB, PcpA, PhtE and Ply of S. Pneumoniae in Three Groups of Children.

Twenty two otitis prone, 13 AOMTF and 20 non-otitis prone children had paired serum samples obtained at their acute (at the time of AOM) and convalescent stage (3 weeks later). In all three groups of children, IgG antibody levels to 4 of the 5 proteins in the acute vs. convalescence stage showed no significant rise in antibody (the exception was PhtE protein in AOMTF children where a significant difference was found, p=0.04) (Table 1). However wide individual variation of the antibody levels in acute and convalescent stage sera were notable, with some children in all 3 groups showing two fold rises in antibody to one or more antigens (Table 2).

Antibody Level in Non-Otitis Prone and Otitis-Prone Children with Age

FIG. 5 shows the IgG antibody levels against PhtD, LytB, PcpA, PhtE and Ply at the time of routine non-AOM visits in prospectively followed non-otitis prone and otitis prone children at 6-24 months of age. The data shown are from 150 non-otitis prone children and 10 otitis-prone children. In the non-otitis prone children, the IgG antibody levels rose significantly (p<0.001) over time for all the proteins except LytB (p=0.075). In comparison, the otitis prone children did not mount significant changes in IgG antibody level over time for any of the five proteins (p=0.40 for protein PhtD, p=0.39 for LytB, p=0.11 for PcpA, p=0.09 for PhtE and p=0.42 for Ply).

These data show that otitis prone children and children with AOMTF have significantly lower antibody levels to Spn proteins at the onset of AOM compared to non-otitis prone children, suggesting that prior exposures to Spn did not elicit or elicited a less robust adaptive immune response as reflected in serum antibody levels. This finding suggests that immunologically, otitis prone and AOMTF children are similar but their responses are different as compared to non-otitis prone children. Also, the amount of serum antibody to the 5 Spn antigens studied increased significantly more slowly in otitis prone children than in non-otitis prone children. Slower acquisition of antibody following natural exposure by NP colonization among otitis prone children is consistent with the observation of an impaired immune response among otitis prone children following otopathogen exposure. These data also shows that otitis prone children and children with AOMTF do not differ from non-otitis prone children in their serum antibody response to AOM. It appears that AOM is not an immunizing event for the majority of children in any of the three groupings, at least in the age range up to 3 years old (as were studied here).

The antigen specific immune responses observed against Spn confirm and extend the observations of others for otitis prone children, contradict some earlier reports and provide much new data. Freijd et al(72) described serum anti-Spn polysaccharide antibody to serotypes 3, 6A and 23 in 15 otitis prone children at 30 months of age compared to age matched control children and adults. They found significantly lower antibody to serotypes 6A and 23 among otitis prone children. Prellner et al(73) measured serum anti-Spn polysaccharide antibody to serotypes 6A, 19 and 23 in 15 otitis prone children and found that 60% of the children had no detectable antibody. Even at 6 years of age the levels of antibody to the 6A polysaccharide in otitis prone children were lower than non-otitis prone children. Hotomi et al(74) evaluated 36 otitis prone (mean age 18 months old) and 20 non otitis prone children for serum antibody responses to NTHi OMP P6 and Spn polysaccharide (using the 23 valent Spn vaccine as antigen). 55% of the otitis prone children had lower antibody responses to P6 and 48% had lower responses to Spn polysaccharide. Yamanaka and Faden in their 1993 studies(75; 76) and Bernstein et al(77) found similar diminished serum and/or mucosal antibody levels to another otopathogen, NTHi, in otitis prone children. To our knowledge this is the first report of serum antibody responses to Spn proteins in otitis prone and in AOMTF children.

These observations regarding anti-PhtD, LytB, PcpA, PhtE and Ply antibody responses in otitis prone children associated with AOM supports the generally held explanation for the otitis prone state: These children have a specific immunologic deficiency in antibody response to Spn and other otopathogens when the exposure occurs via the natural NP route.

As noted in Example 1, otitis prone children have a deficiency in functional T helper cells and T memory cell in response to Spn and NTHi antigens (unpublished results)(82). The antibody responses in these children to parenteral vaccination with diphtheria, tetanus and pertussis were not reduced and these findings are consistent with the observations of Prellner et al (83) and Wiertsma et al (84) who also found that otitis prone children mount normal serum antibody responses to vaccination to measles and other pediatric vaccines. Therefore, the immune dysfunction in otitis prone children occurs with natural exposure to otopathogens and not with parenteral vaccination. Adequate immune responses to Spn conjugate vaccines observed to occur in otitis prone children support this conclusion.(85; 86)

Comparing acute and convalescent antibody levels to the studied Spn proteins, the overall GMTs did not show a significant rise in otitis prone, AOMTF or non-otitis prone children. This is largely due to large variation in individual child immune responses. Indeed, some children did show higher convalescent titers while others showed lower titers and some remained the same. Most likely these results are due to differences in the length of NP carriage of Spn before AOM infection ensued. Those with longer carriage may achieve a peak in antibody response before the onset of AOM and they may show steady or falling antibody levels in acute to convalescent sera. Other children may have a brief time of NP carriage before the onset of AOM and they show rising acute to convalescent antibody levels. These results indicate that the different antigens elicit different antibody response profiles, possibly reflecting their different antigenicity in young children when the protein is presented to the child host in a natural way by asymptomatic colonization or AOM infection. Similar observations were made when antibody responses to NTHi proteins were evaluated and other groups have also observed this variability in acute to convalescent antibody levels surrounding an AOM event (87-89) Soininen et al studied the natural development of antibodies to Spn polysaccharide types 1, 6B, 11A, 14, 19F and 23F associated with NP colonization and AOM in a cohort of 329 children followed during their first 2 years of life.(90) Antibodies increased modestly but significantly over time; serotypes 11A and 14 were more immunogenic at a younger age. They found that antibody levels were equal after NP colonization or AOM. However in a later study involving the same children Soininen et al described the findings as indicating that antibody rises >2 fold were relatively infrequent following AOM with variation attributable to age of the child and the serotype of Spn.(89)

In a corresponding study, the gradual acquisition over time of antibody to the same five Spn proteins studied here as well as to three NTHi proteins (Protein D, P6 and OMP26) in healthy children was noted.(69; 87) In this study, otitis prone children failed to demonstrate or had a significantly slower age related rise in antibody to all five Spn proteins.

In conclusion, these results provide further information on the immunological response of otitis prone children. Immunological hyporesponsiveness in otitis prone children against Spn antigens was observed. Children with AOMTF were also shown to behave immunologically similar to otitis prone children. The administration of a vaccine composition comprising at least one or more of PhtD, PhtE, PcpA, LytB and detoxified pneumolysin (e.g., PlyD1) by the parenteral route (optionally, with an adjuvant) may be used to mitigate the immunological hyporesponsiveness noted following natural exposure to S. pneumoniae.

Example 3

The circulating frequencies of Spn antigen-specific memory B-cells in sera samples obtained from a number of the otitis-prone and non-otitis prone children from the study referenced in Example 1 were assessed and compared. From the total study population of about 387 children, 22 children were studied here: 10 otitis-prone children were identified for study here (based on the availability of sufficient PBMC samples); and 12 non-otitis prone children, with 1 or 2 AOMs and of a similar age to the otitis-prone children were randomly selected to serve as controls. Clinical characteristics of the children are set out in Table 3.

Antigen-specific (PhtD, PhtE, LytB, PcpA, Ply) and total IgG secreting cells were quantified by an (in-house standardized) ELISPOT assay in which memory B-cells were stimulated in vitro to differentiate into antibody-secreting cells (ASC). Briefly, one million thawed PBMC were placed in each well of a 24-well plate containing 1 ml of complete media alone or complete media containing 1 μg/ml of pokeweed mitogen. Cells were kept at 37° C. for 3-days for differentiation, washed with complete media, counted and distributed onto overnight antigen-coated (10 μg/ml) 96-well ELISPOT plates (Millipore). Plasma cell differentiation was optimized with the help of flow cytometric evaluation of the differentiated cells (data not shown). For the detection of total IgG-secreting cells, wells were pre-coated with monoclonal anti-human IgG (MT91/145; Mabtech) at 10 μg/ml in PBS. As a negative control wells were left untreated or coated with same amount of bovine serum albumin (BSA). Plates were blocked with 10% FBS in RPMI 1640 for 30 min at 37° C. Stimulated PBMC were counted and 5×10⁵ cells were resuspended in 200 μl of fresh complete RPMI media before distributing them onto control and antigen-coated wells. Plates were then incubated at 37° C. in a 5% CO₂ incubator overnight and then washed with PBS at least 5-times. Next, 100 μl of 1 μg/ml biotinylated anti-human IgG antibodies (MT78/145; Mabtech) were added to the wells and incubated for an hour. After washing streptavidin-alkaline phosphatase conjugate (1:1000) was added to the wells and incubated for an hour at 37° C. Plates were then washed 5-times with PBS before developing it with substrate (BCIP/NBT; Mabtech). Because of the low frequencies of antigen-specific ASCs, developed spots were manually counted with the help of dissection microscope. Antigen-specific data was expressed as a percentage of antigen-specific memory B-cells and was calculated per million of PBMC as follows: % Ag-specific MBC=(No. antigen-specific spots/No. of total Ig spots)×100.

Antigen-specific IgG titers in the serum of these two groups of children were measured by ELISA performed substantially similar to that described in Example 1, albeit plates were coated with 0.5 μg/ml of antigen and affinity purified goat anti-human IgG, IgM or IgA antibody conjugated to horseradish-peroxidase (Bethyl Laboratories, Inc., Montgomery, Tex.) were used as secondary antibodies.

All data was statistically analyzed using Graph Pad Prism software. Two tailed P values for the data were calculated using Mann Whitney Test.

A summary of the results are set out in FIG. 6 (A, B, C). Percentages of memory B-cells specific to the 5 Spn antigens (PhtD, PhtE, LytB, PcpA, Ply) present in samples from the otitis prone children and non-otitis prone children are shown in FIG. 6A. In sharp contrast the non-otitis prone group, otitis prone children had a marked reduction of circulating Spn specific memory B-cells after an AOM or NP colonization (FIG. 6A). In particular, significantly lower percentages of memory B-cells producing antigen-specific IgG were observed against antigens PhtD, PhtE and PlyD1 (P<0.02). Otitis prone children also showed an overall lower percentage of memory B-cells specific to LytB, although the difference was not statistically significant (p=0.1). No statistically significant difference was found in the percentage of PcpA-specific memory B-cells in the samples from the otitis prone and the non-otitis prone groups (FIG. 6A). Similarly, the total number of IgG-secreting cells present in the two groups did not differ (data not shown).

Serum IgG levels to Spn antigens in the respective groups are shown in FIG. 6B. As compared to the sera from the children in the otitis prone group, IgG titers to PhtD, PcpA and PhtE were significantly higher in the sera from the children in non-otitis group (P<0.05). Ply levels were lower and did not differ in a statistically significant manner between the groups (FIG. 6B). LytB antibody titers were the lowest among all antigens tested in both of the cohorts (FIG. 6B).

In this study, a reduced percentage of memory B-cells circulating in the blood of otitis prone children following AOM and/or NP colonization was noted (FIG. 6A). After encounter of antigen with naive B-cells, antigen-specific memory B-cells and antibody secreting cells are generated in the secondary lymphoid structures that transit through the blood to bone marrow, spleen, or target tissues such as respiratory tract (16). Since serum antibody levels are maintained by memory B-cells (31), by analyzing the percentages of generated antigen-specific memory B-cells, a more precise immunological explanation for lower antibody levels in otitis prone children provided. To confirm the association of lower frequencies of memory B-cells with serum antibody levels, Spn specific antibody titers were measured and found to be significantly lower in otitis prone children (FIG. 6B), similar to the results obtained in the study set out in Example 1 using sera samples from a different cohort of non-otitis prone children (n=15) and otitis-prone children (n=13) following AOM or NP colonization. Overall, the trend of higher Spn antigen specific titer results noted here in non-otitis prone children is consistent with that seen in the cohort evaluated in Example 1, though the exact results in terms of statistically significant differences between groups for antigen specific responses are different in some cases. For example, the small group of children evaluated here did not show any differences in Ply-specific antibody titers. While antibody responses and B-cell generation to a particular protein antigen following bacterial colonization and/or AOM may vary among individual children, a lesser degree of variation is expected with vaccination.

As shown in Example 1, otitis prone children have suboptimal pneumococcal antigen-specific memory CD4+ T-cell responses (96). Findings from this study confirm those from the earlier Examples (i.e., that otitis prone children may develop some antibody responses) since antibodies and memory B-cells were detectable among these children after AOM and NP colonization with otopathogens (FIG. 6A-B). However, in the absence of antigen-specific memory B-cell generation and/or memory CD4+ T-cell generation, the antibody levels wane and otitis prone children are unable to maintain adequate serum antibody levels and become susceptible to repeat AOM infections.

Pneumococcal polysaccharide-conjugate vaccination is helpful in boosting protective levels of anti-polysaccharide antibodies (86); however, serotype variation limits the protective efficacy of strain specific anti-polysaccharide antibodies (95). Moreover, despite the fact that otitis prone children can induce serotype specific antibodies to conjugate vaccines, repeated infections are common among this vulnerable group (86), indicating that serotype-neutralizing immunity is brief and incomplete.

Interestingly, the percentage of circulating PhtD specific memory B-cells correlated with serum PhtD levels (FIG. 6C). A difference in the percentages of antigen-specific B-cells and serum antibodies levels to PcpA and PlyD1 was observed (FIG. 6A-B).

In conclusion, in respect of the antigens evaluated here, otitis-prone children have a significantly lower memory B-cell generation that can differentiate into antibody secreting cells. The clinical relevance of the finding is clear. Antigen specific memory B-cells act as reservoirs for serum antibody maintenance that upon antigen re-encounter can proliferate into ASCs leading to an increase in the serum antibody levels. We found that otitis prone children do not lack total IgG-secreting cells. Furthermore our flow cytometry results showed that in response to polyclonal stimulation, otitis prone children do not have mechanistic dysfunction in the transformation of memory B-cells (CD19+IgD−) to antibody secreting plasma-cells (CD27+CD38+CD138+) (data not shown).

These data show that Spn antigen-specific responses are seen in both non-otitis prone and otitis-prone children following AOM or NP colonization. Although diminished responses are seen in otitis-prone children, responses are nonetheless seen in these children following a natural infection or colonization supporting the administration of a vaccine composition comprising at least one or more of PhtD, PhtE, PcpA, LytB and detoxified pneumolysin (e.g., PlyD1) as described earlier (e.g., Example 2) to mitigate the immunological hyporesponsiveness noted following natural exposure to S. pneumoniae.

While example methods, proteins, compositions and other features have been described, it is not the intention of the applicants to restrict or in any way limit the scope of this invention, disclosure or application. Modifications, alterations and variations will be readily apparent to those of skill in the art. Therefore, this disclosure is not limited to the specific details, the representative apparatus and examples shown and described herein. A sequence listing has been filed herewith and is considered part of this disclosure.

The contents of all references cited above are incorporated herein by reference. Use of singular forms herein, such as “a” and “the”, does not exclude indication of the corresponding plural form, unless the context indicates to the contrary. Thus, for example, if a claim indicates that use of “a” X or Y, it can also be interpreted as covering use of more than one X or Y unless otherwise indicated. To the extent that the term (or) is used in the description or claims (e.g., A or B) it is intended to mean “A or B or both”. In circumstances where the intention is to indicate “only A or B but not both” then the term “only A or B but not both” will be employed. Thus, the term “or” herein is used in the inclusive and not the exclusive sense.

Other embodiments are within the following claims.

TABLE 2* >2 fold increase in antibody at Group (#) of Acute Convalescence convalescence stage Proteins children IgG titers (95% Upper & lower confidence interval) % of children PhtD Otitis-prone 1.8 × 10⁵ 1.4 × 10⁵ 24%  (4.1 × 10⁴-7.92 × 10⁵) (3.9 × 10⁴-5.1 × 10⁵) AOMTF 7.9 × 10⁵ 8.2 × 10⁵ 15% (6.3 × 10⁴-1.0 × 10⁷) (7.7 × 10⁴-8.7 × 10⁶) Non otitis-prone 3.9 × 10⁵ 6.1 × 10⁵ 35% (1.2 × 10⁵-1.3 × 10⁶) (1.8 × 10⁵-2.0 × 10⁶) LytB Otitis-prone ^(a)327 ^(a)275 20% (157-682) (115-658) AOMTF ^(b)260 ^(b)803 33%  (30-2275)  (137-4686) Non otitis-prone ^(a, b)4487   ^(a, b)5451   33%     (1711-1.1 × 10⁴)     (2105-1.4 × 10⁴) PcpA Otitis-prone 6.6 × 10⁵ 6.8 × 10⁵ 29% (1.39 × 10⁵-3.16 × 10⁶) (1.11 × 10⁵-4.21 × 10⁶) AOMTF 5.1 × 10⁵ 6.9 × 10⁵ 36% (3.9 × 10⁴-1.1 × 10⁷) (8.7 × 10⁴-2.3 × 10⁷) Non otitis-prone 4.8 × 10⁵ 4.6 × 10⁵ 25% (1.2 × 10⁵-1.9 × 10⁶) (1.2 × 10⁵-1.7 × 10⁶) PhtE Otitis-prone ^(a)1.3 × 10⁴   ^(a)1.4 × 10⁴   32%     (3315-5.8 × 10⁴)     (3474-6.3 × 10⁴) AOMTF ^(b, c)1.8 × 10⁴    ^(c)2.2 × 10⁴   23%     (3974-8.6 × 10⁴)     (3374-1.4 × 10⁵) Non otitis-prone ^(a, b)1.5 × 10⁵    ^(a)1.1 × 10⁵   19% (5.2 × 10⁴-4.5 × 10⁵) (3.2 × 10⁴-4.3 × 10⁵) PlyD1 Otitis-prone ^(a)1.6 × 10⁴   8578 40%     (5861-4.4 × 10⁴)     (1852-3.9 × 10⁴) AOMTF 1.1 × 10⁴ 8534 18%     (2140-6.0 × 10⁴)     (1675-4.3 × 10⁴) Non otitis-prone ^(a)6.45 × 10⁴   5.46 × 10⁴  0% (3.4 × 10⁴-1.2 × 10⁵) (3.0 × 10⁴-9.6 × 10⁴) *Comparison of geometric mean titer of IgG antibody in the serum samples of 22 otitis prone, 13 AOMTF and 20 non-otitis prone children at their acute vs. convalescence stage. Significant difference (p value < 0.05) found: ^(a)Otitis prone vs Non-otitis prone; ^(b)AOMTF vs Non-otitis prone; ^(c)Acute vs. convalescence serum

TABLE 3 Characteristics of study subjects Otitis Prone Non-Otitis Prone (n = 10) (n = 12) P value Gender Male 6 7 1.00 Female 4 5 1.00 Mean Age (mos.) 13.3 12.1 0.50 # AOM Episodes ≥3 in 6 months 5 0 0.01 ≥4 in 12 months 5 0 0.01 Total number of AOM Episodes 1-3 3 4 1.00 4-5 6 0 0.003 6 or more 1 0 0.45 PET Insertion 4 0 0.03 Breast Feeding ≥6 months 5 8 0.67

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1-38. (canceled)
 39. A method comprising administering a therapeutically effective amount of a composition comprising at least one of Streptococcus pneumoniae PhtD, PhtE, PcpA, LytB and detoxified pneumolysin, or an immunogenic fragment thereof, at least once to said subject.
 40. The method of claim 39, wherein the subject has previously experienced at least one episode of acute otitis media.
 41. The method of claim 40, wherein the subject has experienced three or more episodes of acute otitis media within a period of six months or has experienced four or more episodes of acute otitis media within a period of 12 months.
 42. The method of claim 39, wherein the subject has or is at risk for developing acute otitis media.
 43. The method of claim 42, wherein the subject has acute otitis media.
 44. The method of claim 39, wherein administration of the composition elicits or enhances the production of antigen specific CD4+ T-cells.
 45. The method of claim 44, wherein administration of composition elicits or enhances the production of antigen specific CD4+ T-cells producing IFN-γ, IL-4, IL-2 and/or IL-17a.
 46. The method of claim 45, wherein percentage of antigen specific CD4+ T-cells producing IFN-γ, IL-4, IL-2 and/or IL-17a increases relative to the percentage existing immediately preceding the administration of the composition.
 47. The method of claim 39, wherein administration stimulates the production of IFN-γ, IL-2, IL-4 and/or IL-17a cytokines.
 48. The method of claim 39, wherein the composition further comprises at least one adjuvant.
 49. The method of claim 39 wherein the composition comprises at least two, at least three, at least four, or at least five of Streptococcus pneumoniae PhtD, PhtE, PcpA, LytB and detoxified pneumolysin, or an immunogenic fragment thereof.
 50. The method of claim 39 wherein the detoxified pneumolysin is a mutant pneumolysin protein comprising amino acid substitutions at positions 65, 293 and 428 of the wild type sequence.
 51. The method of claim 50, wherein the three amino acid substitutions comprise T₆₅→C, G₂₉₃→C, and C₄₂₈→A.
 52. The method of claim 39, wherein the subject has experienced an episode of acute otitis media resulting from a S. pneumoniae infection and failed to achieve bacterial eradication and/or resolution of symptoms after at least 48 hours of antibiotic therapy.
 53. The method of claim 39, wherein the subject has experienced an episode of acute otitis media (AOM) resulting from a S. pneumoniae infection and within 14 days of completing an antibiotic treatment course for the AOM, the symptoms of AOM returned. 